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PubMed2000

Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments.

Forty strains of Gram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy's Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 16S rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to Arthrobacter: The other two strains appeared to be most closely related to Kocuria. The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological, physiological and biochemical traits of the subsurface strains were consistent with those of Arthrobacter, Micrococcus and genera recently separated from Micrococcus, such as Kocuria. Some of the subsurface strains were phylogenetically closely related to certain species of Arthrobacter. (16S rDNA sequence similarities >99%). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 16S rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to Arthrobacter. also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of Arthrobacter.

Arthrobacter↗
PubMed1976

Classification of micrococci on the basis of deoxyribonucleic acid homology.

The DNA homology relationships of 25 micrococci (15 strains of Micrococcus, eight strains of Sarcina and two strains of Staphylococcus) were studied by the deoxyribonucleic acid hybridization method using nuclease S1, an endonuclease specific for single-stranded DNA molecules. Nineteen of the strains were classified into three groups. Group I contained Micrococcus lysodeikticus IAMI056, M. luteus IAMI1010, M. flavus IAMI2005 and IAMI2006, Sarcina flava IAMI2007 and IAMI1006. S. subflava IAMI2009, S. lutea ATCC381, and ATCC382, and M. luteus IAMI1006. Group II contained M. roseus IAMI315, ATCC412, ATCC185 and IAMI295. Group III contained S. lutea IAMI099, IFO3232 and ATCC383, M. varians ATCC399 and Staphylococcus lactis ATCC15306. Micrococcus luteus IAMI097, M. varians ATCC19099 and ATCC19100, M. conglomeratus IAMI459 and IAMI470, and St. aureus IAMI011 could not be assigned to any of the three groups. The grouping corresponds to that derived from the results of differential lysis by lysozyme, 'lytic enzyme 2' from Cytophaga sp., or Streptomyces albus G enzyme; and to types of peptidoglycan in the cell walls and genetic transformation. The usefulness of classification based on sensitivity to various lytic enzymes was demonstrated. Group I probably coincides with M. luteus of Bergey's Manual of Determinative Bacteriology (1974), and groups II and III with M. roseus and M. varians respectively.

DNA, Bacterial↗
PubMed2003

Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.

Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99.8% and DNA-DNA similarity of 71% with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 78orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (= MTCC 3702T = DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.

Antarctic Regions↗
PubMed2003

Reclassification of ATCC 9341 from Micrococcus luteus to Kocuria rhizophila.

Strain ATCC 9341, currently known as Micrococcus luteus, has been designated as a quality-control strain in a number of applications. It is also cited as the standard culture in several official methods and manuals, as well as the Code of Federal Regulations. Over the years, it has become apparent that ATCC 9341 does not resemble other M. luteus strains; however, its phenotypic characteristics alone were ambiguous. Recently, a polyphasic study was performed in which molecular data were combined with cytochemical properties and physiological characteristics. The results clearly indicate that ATCC 9341 is a member of the genus Kocuria. Thus, it is proposed to reclassify ATCC 9341 as Kocuria rhizophila and to alert users worldwide of this name change.

DNA, Bacterial↗
PubMed2003

Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment.

Three bacterial strains were isolated from sea-water samples taken from Amursky Bay of the Gulf of Peter the Great, East Sea. The isolates, designated KMM 3670, KMM 3673(T) and KMM 3928, were Gram-positive, non-motile, aerobic, non-spore-forming, irregular, rod-shaped actinobacteria. They grew well at mesophilic temperatures and neutral pH and tolerated up to 10 % NaCl, although salt was not essential for growth. The three strains shared all morphological properties and most physiological characteristics tested. Based on subsequent chemotaxonomic and phylogenetic analyses, it was evident that the strains represented a distinctive taxon in the family Microbacteriaceae. The strains contained a major amount of menaquinone with 11 isoprene units; lysine and ornithine were the major cell-wall diamino acids. In 16S rDNA analysis, the three strains formed an independent phylogenetic lineage within the tree encompassed by members of the family Microbacteriaceae. It is notable that the tested strains form the first described taxon of Microbacteriaceae that inhabits a marine aquatic environment. The three strains evidently merit recognition as a single species of a novel genus in the family Microbacteriaceae, for which the name Salinibacterium amurskyense gen. nov., sp. nov. (type strain, KMM 3673(T)=KCTC 9931(T)) is proposed.

Korea↗
PubMed2003

Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain.

A coccoid- to ovoid-shaped, Gram-positive bacterial strain, designated C3H-21(T), was isolated from the liver of the laboratory mouse strain C3H/He and characterized by a polyphasic approach. The peptidoglycan type was variation A4gamma with meso-diaminopimelic acid as the diagnostic cell-wall diamino acid and an interpeptide bridge of D-asp-D-Glu. The isolate contained menaquinone MK-7 (88 %) as the major component of the quinone system and minor amounts of menaquinone MK-8 (9 %) and menaquinone MK-6 (3 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, unidentified glycolipids and unidentified phospholipids. The fatty acid profile contained predominantly anteiso-C(15 : 0) and significant amounts of iso-C(16 : 0), iso-C(14 : 0,) anteiso-C(17 : 0) and C(19 : 0). The polyamine pattern consisted of spermine and spermidine as the major compounds. Genomic fingerprints clearly distinguished strain C3H-21(T) from other Brachybacterium species. The isolate shared the highest 16S rDNA sequence similarities with members of the genus Brachybacterium, in particular Brachybacterium sacelli LMG 20345(T), Brachybacterium nesterenkovii DSM 9573(T), Brachybacterium rhamnosum LMG 19848(T), Brachybacterium alimentarium CNRZ 925(T) and Brachybacterium fresconis LMG 20336(T) (97.8-97.2 %). The results of biochemical/physiological characterization, chemotaxonomic characteristics and REP-PCR-generated fingerprints demonstrated that the isolate represents a novel species of the genus Brachybacterium, for which the name Brachybacterium muris (type strain C3H-21(T)=DSM 15460(T)=CCM 7047(T)) [corrected] is proposed.

Animals↗
PubMed2004

Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment.

An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation. The isolate, designated KMM 3905T, was Gram-positive, aerobic, non-motile and coccoid. The strain tolerated up to 15 % NaCl in growth media, although its presence was not essential for growth. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification in the genus Kocuria. The strain formed an independent phylogenetic line in the 16S rRNA gene tree encompassed by members of Kocuria. Comparison of phenotypic characteristics also supported its assignment to a novel species within Kocuria. The name Kocuria marina sp. nov. (type strain KMM 3905T = KCTC 9943T) is proposed for this halotolerant actinobacterium from the marine environment.

Aerobiosis↗
PubMed2004

Xylanibacterium ulmi gen. nov., sp. nov., a novel xylanolytic member of the family Promicromonosporaceae.

A bacterial strain designated XIL08(T) was isolated from an elm tree affected by Dutch elm disease. Strain XIL08(T) is Gram-positive, aerobic, rod-shaped and non-motile. The complete 16S rDNA sequence of this micro-organism was obtained and phylogenetic analysis based on the neighbour-joining method indicated that the closest related organism belongs to the genus Xylanimonas of the family Promicromonosporaceae, suborder Micrococcineae. Cell-wall analyses revealed the presence of type A4alpha, L-lys-L-ala-D-Glu peptidoglycan. The cell-wall sugars found were rhamnose in large amounts, fucose, mannose and galactose and traces of arabinose and glucose. HPLC analysis of menaquinones revealed two peaks, the main peak corresponding to MK-9(H(4)) and the smaller one to MK-8(H(4)). The major fatty acid found was anteiso-C(15 : 0). Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The G+C content of the DNA was 72 mol%. Isolate XIL08(T) hydrolysed xylan but not cellulose. Growth was observed with many carbohydrates including acetate and xylan as the only carbon source. Catalase activity was not detected. The data from this polyphasic study suggest that this bacterium belongs to a novel genus of the family Promicromonosporaceae. It is proposed that isolate XIL08(T) (=LMG 21721(T)=CECT 5731(T)) be classified in a new genus, Xylanibacterium gen. nov., as the type strain of Xylanibacterium ulmi sp. nov.

Base Composition↗
PubMed2004

Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir.

Four Gram-positive bacteria, strains A1-17B(T), A1-22(T), A1-3(T) and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17B(T)), Rhodococcus (A1-22(T)) and Arthrobacter (A1-3(T) and A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17B(T) and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa, Rothia mucilaginosa and Rothia nasimurium, were respectively 99.8, 98.0, 96.4 and 95.4 %. Polyphasic taxonomic evidence indicated that strain A1-17B(T) should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus ROTHIA: Strain A1-22(T) formed a coherent cluster with Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA-DNA relatedness values were only 45.5, 35.3, 18.9 and 21.9 %. Strains A1-3(T) and A1-8 shared 99.9 % 16S rDNA sequence similarity, and strain A1-3(T) showed the highest level of 16S rDNA similarity, 96.6 %, to Arthrobacter polychromogenes. Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp. nov. (A1-17B(T)=GTC 867(T)=JCM 11412(T)=DSM 14556(T)), Rhodococcus baikonurensis sp. nov. (A1-22(T)=GTC 1041(T)=JCM 11411(T)=DSM 44587(T)) and Arthrobacter russicus sp. nov. (A1-3(T)=GTC 863(T)=JCM 11414(T)=DSM 14555(T)).

Air Microbiology↗
PubMed2004

Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China.

The taxonomic position of two Gram-positive strains, YIM 70084(T) and YIM 70097(T), isolated from hypersaline soils was determined by a polyphasic approach. Cells of strain YIM 70084(T) are motile cocci, whereas those of strain YIM 70097(T) are non-motile rods. The G+C contents of their DNA are 64.4 and 66.7 mol%. Both strains had chemotaxonomic markers typical of the genus Nesterenkonia and formed a coherent cluster with Nesterenkonia species in a phylogenetic inference based on 16S rDNA sequence analysis, exhibiting less than 97 % similarity to each other and to the other two type strains of the genus. Phylogenetic distinction and differences in the peptidoglycan type, composition of cell-wall sugars, phospholipid patterns, the major menaquinones and other phenotypic characteristics indicate that the strains under study represent two novel species, Nesterenkonia halotolerans sp. nov. (type strain YIM 70084(T)=CCTCC AA 001022(T)=DSM 15474(T)) and Nesterenkonia xinjiangensis sp. nov. (type strain YIM 70097(T)=CCTCC AA 001025(T)=DSM 15475(T)).

Base Composition↗
PubMed2005

Citricoccus alkalitolerans sp. nov., a novel actinobacterium isolated from a desert soil in Egypt.

An actinobacterium, strain YIM 70010T, which was isolated from a desert soil sample collected in Egypt, was subjected to a polyphasic taxonomy study. The organism was alkalitolerant and its optimum growth occurred at pH 8.0-9.0. The isolate contained chemotaxonomic markers that were characteristic of the genus Citricoccus, i.e. the peptidoglycan type Lys-Gly-Glu (variation A4alpha), the predominant menaquinone MK-9(H2) and a polar lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown glycolipids. The major fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The G+C content of the genomic DNA was 63.8 mol%. Strain YIM 70010T exhibited a 16S rRNA gene sequence similarity of 99.6 % and DNA-DNA relatedness value of 56 % with Citricoccus muralis DSM 14442T. The phenotypic characteristics and DNA-DNA relatedness data indicate that strain YIM 70010T can be distinguished from C. muralis (DSM 14442T). Therefore, on the basis of the polyphasic taxonomic data presented, a novel species of the genus Citricoccus, Citricoccus alkalitolerans sp. nov. (type strain, YIM 70010)=CCTCC AA 203008T=DSM 15665T=KCTC 19012T) is proposed.

Bacterial Typing Techniques↗
PubMed2005

Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia.

Two novel actinobacteria isolates, designated YIM 70009T and YIM 70081T, were characterized in order to determine their taxonomic position. Cells of strains YIM 70009T and YIM 70081T were cocci, although only the latter were motile. The G+C contents of their DNAs were 64.0 and 64.5 mol%, respectively. On the basis of chemotaxonomic characteristics and 16S rRNA gene sequence analysis, the two isolates were classified in the genus Nesterenkonia. DNA-DNA hybridization and comparison of phenotypic characteristics revealed that strains YIM 70009T and YIM 70081T differed from each other and from known species. Therefore, it is proposed that they represent two separate novel species of the genus Nesterenkonia: Nesterenkonia sandarakina sp. nov. (type strain, YIM 70009T=CCTCC AA 203007T=DSM 15664T=KCTC 19011T) and Nesterenkonia lutea sp. nov. (type strain, YIM 70081T=CCTCC AA 203010T=DSM 15666T=KCTC 19013T).

Base Composition↗
PubMed2005

Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.

A Gram-positive actinobacterium, previously classified as Kocuria varians, was subjected to a polyphasic taxonomic study. The bacterium showed the peptidoglycan type Lys-Ala3 (variation A3alpha), MK-7(H2) was the major menaquinone and anteiso-C(15 : 0) and anteiso-C(17 : 0) were the major fatty acids. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel species, Kocuria carniphila sp. nov. (type strain, CCM 132T=DSM 16004T), is proposed.

Animals↗
PubMed2006

Nesterenkonia aethiopica sp. nov., an alkaliphilic, moderate halophile isolated from an Ethiopian soda lake.

Strain DSM 17733(T), isolated from the shore of Lake Abjata in Ethiopia, is a heterotrophic, alkaliphilic, moderately halophilic, Gram-positive, strictly aerobic, non-motile,non-endospore-forming bacterium. The organism grows optimally at 30-37 degrees C, pH 9 and 3 % (w/v) NaCl. Analysis of the cell wall showed the presence of murein of the type L-lys-gly-L-Glu, variation A4alpha. The G + C content of the genomic DNA was 69.0 mol%. Sequence analysis of 16S rRNA gene sequence of strain DSM 17733(T) placed the isolate in the genus Nesterenkonia. DNA-DNA hybridization of DSM 17733(T) with those organisms with the closest phylogenetic affiliation, i.e. Nesterenkonia halobia, Nesterenkonia lacusekhoensis and Nesterenkonia xinjiangensis, gave relatedness values of 48.5 %, 63.7 % (repetition, 57.2 %) and 35.7 % (repetition, 29.3 %), respectively. On the basis of both phenotypic and phylogenetic criteria and the low levels of DNA-DNA relatedness with the phylogenetically closest species N. xinjiangensis and N. halobia, it is proposed that the isolate be classified in a novel species, Nesterenkonia aethiopica sp. nov. The type strain is DSM 17733(T) (=CCUG 48939(T)).

Ethiopia↗
PubMed2006

Nesterenkonia jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.

A Gram-positive, non-motile, slightly halophilic actinomycete, strain JG-241T, was isolated from jeotgal, a traditional Korean fermented seafood, and its taxonomic position was investigated by using a polyphasic approach. Strain JG-241T grew optimally at 25-30 degrees C and in the presence of 2-5% (w/v) NaCl. The physiological and biochemical properties of strain JG-241T were distinguishable from those of recognized Nesterenkonia species. Strain JG-241T had a peptidoglycan type based on L-lys-gly-D-Asp. It contained MK-7, MK-8 and MK-9 as the predominant menaquinones and anteiso-C15:0) and anteiso-C17:0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The DNA G+C content was 68.0 mol%. Comparative 16S rRNA gene sequence analysis showed that strain JG-241T falls within the radiation of the cluster comprising Nesterenkonia species. Similarity values between the 16S rRNA gene sequence of strain JG-241T and those of the type strains of Nesterenkonia species ranged from 96.7 to 99.7%. DNA-DNA relatedness data and repetitive extragenic palindromic DNA-PCR genomic fingerprinting patterns showed that strain JG-241T differs genetically from recognized Nesterenkonia species. On the basis of its phenotypic properties and phylogenetic and genetic distinctiveness, strain JG-241T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia jeotgali sp. nov. is proposed. The type strain is JG-241T (=KCTC 19053T=JCM 12610T).

Base Composition↗
PubMed1987

Skin microflora.

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Actinomycetales↗