Nakamurella silvestris sp. nov., a novel actinobacterium isolated from alpine forest soil (original) (raw)

Nakamurella silvestris sp. nov., an actinobacterium isolated from alpine forest soil

International Journal of Systematic and Evolutionary Microbiology, 2016

A Gram-stain-positive, non-motile, catalase-positive and cytochrome c oxidase-negative bacterium, designated strain S20-107 T , was isolated from alpine forest soil. Growth occurred at 0-30 C, at pH 6-9 and in the presence of 0-3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S20-107 T was related to the genus Nakamurella and had the highest 16S rRNA gene sequence similarity with Nakamurella flavida DS-52 T (96.1 %). Strain S20-107 T showed <96.1% 16S rRNA gene sequence similarities to all other recognized members of the genus Nakamurella. The cell-wall peptidoglycan contained mesodiaminopimelic acid. The major whole-cell sugars were glucose, galactose, mannose, arabinose, ribose and rhamnose. The strain contained MK-8(H 4) as the predominant menaquinone and diphosphatidylglycerol, phosphatidylethanolamine and an unidentified aminophospholipid as the major polar lipids. The major cellular fatty acids were anteiso-C 15 : 0 , C 16 : 0 , summed feature 3 (C 16 : 1 !6c and/or C 16 : 1 !7c and/or iso-C 15 : 0 2-OH) and iso-C 16 : 0. The genomic DNA G+C content was 70.5 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-107 T represents a novel species of the genus Nakamurella, for which the name Nakamurella silvestris sp. nov. is proposed. The type strain is S20-107 T (=DSM 102309 T =LMG 29427 T).

Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from bark of Kandelia candel

International journal of systematic and evolutionary microbiology, 2016

A Gram-positive, aerobic, coccus-shaped, non-spore-forming actinobacterium, designated strain 2Q3S-4-2T, was isolated from a surface-sterilized bark of Kandelia candel collected from Cotai Ecological Zones in Macao, China and tested by a polyphasic approach to determine its taxonomic position. Strain 2Q3S-4-2T grew optimally without NaCl at 28-30 °C, pH 7.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 2Q3S-4-2T belonged to the genus Nakamurella and shared the highest 16S rRNA gene sequence similarity with N. flavida DS-52T (96.76 %). The DNA G+C content of strain 2Q3S-4-2T was 67.8 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid and MK-8(H4) was the predominant menaquinone. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), unidentified aminophospholipid (APL) and phosphati...

Saxeibacter lacteus gen. nov., sp. nov., an actinobacterium isolated from rock

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2008

A Gram-positive, cream-coloured, non-motile, rod-shaped actinomycete, designated DLS-10 T , was isolated from a rock collected on the peak of Darangshi Oreum (a small mountain 300 m above sea level) in Jeju, Republic of Korea. The temperature and pH ranges for growth were 4-37 6C and pH 5.1-9.1. The organism grew at NaCl concentrations up to 3 % and had the following chemotaxonomic characteristics: meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, the polar lipids included diphosphatidylglycerol, phosphatidylmethylethanolamine and two unknown phospholipids, the major menaquinone was MK-8(H 4) and the major fatty acids were anteiso-C 15 : 0 , C 16 : 0 , iso-C 16 : 0 and anteiso-C 17 : 0. The DNA G+C content was 74.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism was related to members of the family Nakamurellaceae in the suborder Frankineae. The most closely related described organisms were the type strains of Humicoccus flavidus (97.1 % sequence similarity) and Nakamurella multipartita (95.2 %). On the basis of the morphological, cultural, physiological, chemotaxonomic and phylogenetic evidence presented here, the organism represents a novel genus and species of the family Nakamurellaceae, for which the name Saxeibacter lacteus gen. nov., sp. nov. is proposed. The type strain of Saxeibacter lacteus is DLS-10 T (5KCTC 19285 T 5DSM 19367 T).

Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2006

A reddish orange bacterium, strain K07-05 T , was isolated from soil during a study of the bacterial diversity of a cold desert of the Indian Himalayas and was studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genus Kocuria. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain K07-05 T was closely related to Kocuria rosea DSM 20447 T and Kocuria polaris MTCC 3702 T (98?1 and 97?8 % sequence similarity, respectively), whereas the sequence similarity values with respect to the other Kocuria species with validly published names were between 96?4 and 94?2 %. However, the genomic relatedness, as shown by DNA-DNA hybridization, of strain K07-05 T and K. polaris MTCC 3702 T is 49?5 % and that with K. rosea MTCC 2522 T is 24?0 %. The DNA G+C content of the strain is 75?3 mol%. The above data in combination with the phenotypic distinctiveness of K07-05 T clearly indicate that the strain represents a novel species, for which the name Kocuria himachalensis sp. nov. is proposed. The type strain is K07-05 T (=MTCC 7020 T =DSM 44905 T =JCM 13326 T ).

Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2010

A Gram-stain-positive, coccoid, non-motile, halotolerant actinobacterium, designated YIM 45900T, was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The peptidoglycan type was A4α with an l-Lys–l-Ser–d-Asp interpeptide bridge. The cell-wall sugars contained galactose and fucose. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylinositol, a glucosamine-containing phospholipid and an unknown phospholipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism falls within the radius of the suborder Micrococcineae and its closest phylogenetic neighbours are the genera of the family Dermacoccaceae. Strain YIM 45900T showed 16S rRNA gene sequences similarity values of 93.1–95.9 % with members of the genera Dermacoccus, Demetria and Kytococcus. ...

Nonomuraea jabiensis sp. nov., isolated from arid soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013

A novel actinomycete, strain A4036 T , was isolated from a soil sample collected from the Jabi 28 district in Abuja, Nigeria. The taxonomic position of strain A4036 T was established using a 29 combination of genotypic and phenotypic data. The organism formed extensively branched 30 substrate and aerial hyphae that generated spiral chains of spores with warty-surfaces. The 31 cell wall contained meso-diaminopimelic acid and the cell wall sugars were glucose, 32 madurose, mannose and ribose. The predominant menaquinone was MK-9 (H 4 ). The polar 33 lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, 34 phosphatidylmethylethanolamine, phosphatidylinositol mannoside, hydroxy-phosphatidyl 35 ethanolamine, hydroxy-phosphatidyl methylethanolamine, two unidentified phospholipids and 36 four unidentified glycolipids. The major cellular fatty acids were iso-C 16:0 2OH , iso-C 16:0 and 37 10-methyl C 17:0 . On the basis of 16S rRNA gene sequence similarity studies, strain A4036 T 38 grouped in the genus Nonomuraea, being most closely related to Nonomuraea angiospora 39 (99.05 %), Nonomuraea candida (98.78 %), Nonomuraea kuesteri (98.49 %), Nonomuraea 40 endophytica (98.42 %), Nonomuraea maheshkhaliensis (98.40 %), Nonomuraea turkmeniaca 41 (98.38 %), Nonomuraea helvata (98.29 %), Nonomuraea rubra (98.10 %) and Nonomuraea 42 salmonea (98.06 %). The 16S rRNA gene sequence similarity to other species of the genus 43 Nonomuraea was <98 %. Despite the high 16S rRNA gene sequence similarities, DNA-DNA 44 relatedness and phenotypic data demonstrated that strain A4036 T was clearly distinguished 45 from all closely related Nonomuraea type species. Thus, this isolate is considered to represent 46 a novel species of the genus Nonomuraea, for which the name Nonomuraea jabiensis sp. nov. 47 is proposed. The type strain is A4036 T ( = DSM 45507 T = KCTC 19870 T ).

Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov.

Strain ATCC 39727, which produces the antibiotic A40926 (the natural precursor of the antibiotic dalbavancin), was isolated from a soil sample collected in India, and it was originally classified as a member of the genus Actinomadura on the base of morphology and cell-wall composition. A phylogenetic analysis based on 16S rRNA gene sequences indicates that the strain forms a distinct clade within the genus Nonomuraea, and it is most closely related to Nonomuraea angiospora DSM 43173 T (98.72 % similarity) and Nonomuraea jabiensis A4036 T (98.69 %). The strain forms an extensively branched substrate mycelium and aerial hyphae that form spiral chains of spores with ridged surfaces. The cell wall contains meso-diaminopimelic acid and the whole-cell sugars are glucose, ribose, galactose, mannose and madurose (madurose as the diagnostic sugar). The N-acyl type of muramic acid is acetyl. The predominant menaquinone is MK-9(H 4), with minor amounts of MK-9(H 2), MK-9(H 6) and MK-9(H 0). The polar-lipid profile includes diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylinositol and a series of uncharacterized phospholipids, glycolipids and phosphoglycolipids. The major cellular fatty acids are iso-C 16 : 0 and 10-methyl C 17 : 0. The genomic DNA G+C content is 71.2 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, together with DNA–DNA relatedness between strain ATCC 39727 and closely related type strains, clearly demonstrated that strain ATCC 39727 represents a novel species of the genus Nonomuraea, for which the name Nonomuraea gerenzanensis sp. nov. is proposed. The type strain is ATCC 39727 T (5DSM 100948 T).

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