scholarly journals Micromonospora marina sp. nov., isolated from sea sand

2010 ◽  
Vol 60 (3) ◽  
pp. 648-652 ◽  
Author(s):  
Somboon Tanasupawat ◽  
Suchada Jongrungruangchok ◽  
Takuji Kudo
Keyword(s):  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Differences ◽  
Sea Sand ◽  
Acid Type ◽  
Close Relationship ◽  
Micromonospora Chalcea ◽  
Type Strains ◽  
Fatty Acid Type

Two actinomycete strains, JSM1-1T and JSM1-3, were isolated from sea sand collected in Thailand. Their taxonomic position was determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole cell sugar pattern D, phospholipids type II, and cellular fatty acid type 3b. Phylogenetic analysis of 16S rRNA gene sequences revealed a close relationship between strains JSM1-1T and JSM1-3 (99.8 %), and between JSM1-1T and Micromonospora aurantiaca JCM 10878T (99.3 %), Micromonospora chalcea JCM 3031T (99.0 %), and Micromonospora coxensis JCM 13248 T (99.0 %). However, strains JSM1-1T and JSM1-3 could be clearly distinguished from these type strains by a low DNA–DNA relatedness and by phenotypic differences. On the basis of the data presented, a new species, Micromonospora marina sp. nov., is proposed. The type strain is JSM1-1T (=JCM 12870T =PCU 269T =TISTR 1566T).

scholarly journals Micromonospora humi sp. nov., isolated from peat swamp forest soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1176-1181 ◽  
Author(s):  
Apakorn Songsumanus ◽  
Somboon Tanasupawat ◽  
Chitti Thawai ◽  
Khanit Suwanborirux ◽  
Takuji Kudo
Keyword(s):  
Forest Soil ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Swamp Forest ◽  
Peat Swamp Forest ◽  
Phenotypic Differences ◽  
Peat Swamp ◽  
Close Relationship ◽  
Taxonomic Approach

A novel actinomycete, strain P0402T, was isolated from peat swamp forest soil collected in Thailand. Its taxonomic position was determined by using a polyphasic taxonomic approach. The chemotaxonomic characteristics of this strain matched those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole-cell sugar pattern D, phospholipid type II, and cellular fatty acid type 3b. Phylogenetic analysis based on 16S rRNA gene sequences revealed a close relationship between strain P0402T and Micromonospora coxensis JCM 13248T (99.0 % similarity), Micromonospora eburnea JCM 12345T (99.0 %), Micromonospora marina JCM 12870T (98.9 %), Micromonospora halophytica JCM 3125T (98.7 %), Micromonospora chalcea JCM 3031T (98.7 %), Micromonospora purpureochromogenes JCM 3156T (98.6 %) and Micromonospora aurantiaca JCM 10878T (98.5 %). It could be clearly distinguished from these type strains based on low levels of DNA–DNA relatedness and phenotypic differences. On the basis of the data presented, strain P0402T is suggested to represent a novel species of the genus Micromonospora, for which the name Micromonospora humi sp. nov. is proposed. The type strain is P0402T ( = JCM 15292T  = PCU 315T  = TISTR 1883T).

scholarly journals Amycolatopsis xylanica sp. nov., isolated from soil

2010 ◽  
Vol 60 (9) ◽  
pp. 2124-2128 ◽  
Author(s):  
Jie Chen ◽  
Jin-Jin Su ◽  
Yu-Zhen Wei ◽  
Qiu-Ping Li ◽  
Li-Yan Yu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Taxonomic Status ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Qinghai Province ◽  
Phenotypic Differences ◽  
Separate Branch ◽  
Type Strains ◽  
Sequence Similarities

An actinomycete, designated CPCC 202699T, was isolated from soil in Qinghai province, China, and its taxonomic status was established. Strain CPCC 202699T contained meso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, a phospholipid pattern consisting mainly of phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine, MK-9(H4) as the predominant menaquinone and iso-C16 : 0 (18.8 %), iso-C15 : 0 (18.1 %), iso-C14 : 0 (14.2 %), C16 : 1 cis9 (10.9 %) and C17 : 1 cis9 (10.3 %) as the major fatty acids. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 202699T formed a separate branch within the genus Amycolatopsis. However, strain CPCC 202699T showed low 16S rRNA gene sequence similarities (<97.0 %) with type strains of species with validly published names in the genus Amycolatopsis. On the basis of genotypic and phenotypic differences from the closest phylogenetic neighbours of strain CPCC 202699T, a novel species, Amycolatopsis xylanica sp. nov., is proposed. The type strain is CPCC 202699T (=DSM 45285T =KCTC 19581T =CCM 7627T).

Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 867-872 ◽  
Author(s):  
Herbert Seiler ◽  
Mareike Wenning ◽  
Verena Schmidt ◽  
Siegfried Scherer
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acid Type

A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585T, was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to Bacillus oceanisediminis H2T, Bacillus infantis SMC 4352-1T, Bacillus firmus NCIMB 9366T, Bacillus circulans ATCC 4513T and Bacillus horneckiae DSM 23495T with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA–DNA relatedness values between strain WCC 4585T and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585T is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585T( = DSM 23668T = CCUG 59876T = LMG 25856T).

scholarly journals Serinicoccus chungangensis sp. nov., isolated from tidal flat sediment, and emended description of the genus Serinicoccus

2011 ◽  
Vol 61 (6) ◽  
pp. 1299-1303 ◽  
Author(s):  
Jitsopin Traiwan ◽  
Mi-Hak Park ◽  
Wonyong Kim
Keyword(s):  
Tidal Flat ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Bacterium Strain ◽  
Type Strains

A Gram-positive, halophilic bacterium, strain CAU 9536T, was isolated from a tidal flat sediment in the Yellow Sea, Republic of Korea. Strain CAU 9536T grew optimally at 30 °C, at pH 9.0 and in the presence of 13.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 9536T belonged to the genus Serinicoccus, and showed sequence similarity levels of 99.0 % to Serinicoccus profundi MCCC 1A05965T and 98.0 % to Serinicoccus marinus JC1078T. DNA–DNA relatedness values between strain CAU 9536T and the above two type strains were below 45.0 %. The cell-wall peptidoglycan of strain CAU 9536T was based on meso-diaminopimelic acid, in contrast to those of S. profundi and S. marinus. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. Whole-cell hydrolysates contained mainly glucose and ribose. The major isoprenoid quinone was menaquinone MK-8 (H4), and the predominant cellular fatty acid was iso-C15 : 0. The DNA G+C content of strain CAU 9536T was 73.5 mol%. Based on phenotypic, chemotaxonomic and genotypic data, strain CAU 9536T is considered to represent a novel species of the genus Serinicoccus, for which the name Serinicoccus chungangensis sp. nov. is proposed. The type strain is CAU 9536T ( = KCTC 19774T = CCUG 59777T).

scholarly journals Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment

2011 ◽  
Vol 61 (2) ◽  
pp. 281-285 ◽  
Author(s):  
Mi-Hak Park ◽  
Jitsopin Traiwan ◽  
Min Young Jung ◽  
Yun Sung Nam ◽  
Ji Hoon Jeong ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).

scholarly journals Pseudonocardia babensis sp. nov., isolated from plant litter

2010 ◽  
Vol 60 (10) ◽  
pp. 2336-2340 ◽  
Author(s):  
Yayoi Sakiyama ◽  
Nguyen K. N. Thao ◽  
Hoang V. Vinh ◽  
Nguyen M. Giang ◽  
Shinji Miyadoh ◽  
...  
Keyword(s):  
National Park ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Plant Litter ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Low Levels ◽  
Type Strains

A novel actinomycete, designated strain VN05A0561T, was isolated from plant litter collected at Ba Be National Park, Vietnam. The substrate mycelia and spore chains fragmented in a manner similar to nocardioform actinomycetes; the spores had smooth surfaces and were rod-shaped. Strain VN05A0561T had the following chemotaxonomic characteristics: meso-diaminopimelic acid in the cell-wall peptidoglycan, arabinose and galactose as characteristic sugars, MK-8(H4) as the major isoprenoid quinone, phosphatidylcholine as the diagnostic phospholipid and iso-C16 : 0 as the major cellular fatty acid. Strain VN05A0561T shared low levels of 16S rRNA gene sequence similarity (<97 %) with the type strains of recognized species of the genus Pseudonocardia and could be differentiated from its closest phylogenetic relatives based on phenotypic characteristics. These results suggested that strain VN05A0561T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia babensis sp. nov. is proposed. The type strain is VN05A0561T (=VTCC-A-1757T=NBRC 105793T).

scholarly journals Asanoa iriomotensis sp. nov., isolated from mangrove soil

2005 ◽  
Vol 55 (2) ◽  
pp. 725-727 ◽  
Author(s):  
Tomohiko Tamura ◽  
Takeshi Sakane
Keyword(s):  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Monophyletic Cluster ◽  
Mangrove Soil ◽  
Acid Type ◽  
The Family ◽  
Agar Surface ◽  
The 16S Rrna Gene ◽  
Fatty Acid Type

During a study of the distribution of actinomycetes in a mangrove zone, a strain forming spore chains borne on the tip of short sporophores arising directly from the agar surface was isolated from soil. The isolate contained glutamic acid, glycine, alanine and meso-diaminopimelic acid as cell-wall amino acids, menaquinone MK-10(H6, H8), fatty acid type 2d and xylose in the whole-cell hydrolysate. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the members of the genus Asanoa in the family Micromonosporaceae. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA hybridization, a novel species of the genus Asanoa is proposed for strain TT 97-02T (=NBRC 100142T=DSM 44745T), Asanoa iriomotensis sp. nov.

scholarly journals Paenibacillus puldeungensis sp. nov., isolated from a grassy sandbank

2011 ◽  
Vol 61 (3) ◽  
pp. 670-673 ◽  
Author(s):  
Jitsopin Traiwan ◽  
Mi-Hak Park ◽  
Wonyong Kim
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Type Strains

The taxonomic position of a Gram-stain-positive, rod-shaped, endospore-forming, facultatively anaerobic bacterial strain, CAU 9324T, isolated from a grassy sandbank was investigated by using a polyphasic approach. Strain CAU 9324T grew optimally at 30 °C and pH 6.0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major isoprenoid quinone was menaquinone-7 (MK-7). The polar lipid profile consisted of diphosphatidylglycerol as the major component. The predominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content of strain CAU 9324T was 48.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain belonged to the genus Paenibacillus, showing <96.4 % similarity to the type strains of all recognized Paenibacillus species. On the basis of phenotypic, chemotaxonomic and genotypic data, strain CAU 9324T was considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus puldeungensis sp. nov. is proposed. The type strain is CAU 9324T (=KCTC 13718T =CCUG 59189T).

scholarly journals Natribacillus halophilus gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium isolated from soil

2012 ◽  
Vol 62 (2) ◽  
pp. 289-294 ◽  
Author(s):  
Akinobu Echigo ◽  
Hiroaki Minegishi ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
Ron Usami
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Garden Soil ◽  
Rrna Gene ◽  
Moderately Halophilic ◽  
Acid Type ◽  
Optimum Ph ◽  
Sequence Similarities

A moderately halophilic and alkalitolerant bacterium, designated strain HN30T, was isolated from garden soil in Japan. Cells of strain HN30T were motile, endospore-forming, aerobic, rod-shaped and Gram-positive, and contained A1γ meso-diaminopimelic acid-type murein. Growth occurred in 7–23 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.5–10.0 (optimum, pH 8.0–8.5) and at 20–40 °C (optimum, 30 °C). The isoprenoid quinone was menaquinone-7. The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of strain HN30T was 47 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN30T was most closely related to Geomicrobium halophilum BH1T (93 % sequence similarity). 16S rRNA gene sequence similarities with other recognized species were less than 89 %. Phylogenetic and phenotypic characteristics indicated that strain HN30T represents a novel species in a new genus, for which the name Natribacillus halophilus gen. nov., sp. nov. is proposed; the type strain is HN30T ( = JCM 15649T = DSM 21771T).

Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3280-3286 ◽  
Author(s):  
Iris Kuo ◽  
Jimmy Saw ◽  
Durrell D. Kapan ◽  
Stephanie Christensen ◽  
Kenneth Y. Kaneshiro ◽  
...  
Keyword(s):  
Type Species ◽  
Original Description ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Whole Cells ◽  
Link Type ◽  
Decaying Wood ◽  
Type Strains

Strain IK-1T was isolated from decaying tissues of the shrub Wikstroemia oahuensis collected on O‘ahu, Hawai‘i. Cells were rods that stained Gram-negative. Gliding motility was not observed. The strain was oxidase-negative and catalase-positive. Zeaxanthin was the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-1T grown on R2A were iso-C15 : 0 and one or both of C16 : 1ω7c and C16 : 1ω6c. Based on comparisons of the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strains were Flavobacterium rivuli WB 3.3-2T and Flavobacterium subsaxonicum WB 4.1-42T, with which IK-1T shares 93.84 and 93.67 % identity, respectively. The G+C content of the genomic DNA was 44.2 mol%. On the basis of distance from its nearest phylogenetic neighbours and phenotypic differences, the species Flavobacterium akiainvivens sp. nov. is proposed to accommodate strain IK-1T ( = ATCC BAA-2412T = CIP 110358T) as the type strain. The description of the genus Flavobacterium is emended to reflect the DNA G+C contents of Flavobacterium akiainvivens IK-1T and other species of the genus Flavobacterium described since the original description of the genus.

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