Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment

2011 ◽  
Vol 61 (6) ◽  
pp. 1375-1381 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vasily I. Svetashev ◽  
Nataliya I. Kalinovskaya
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Biochemical Characterization ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Physiological And Biochemical ◽  
Sequence Similarities

An aerobic, Gram-stain-negative, non-pigmented, non-motile bacterium, strain KMM 9031T, was isolated from a sandy sediment sample collected from the shore of the Sea of Japan and subjected to phenotypic and phylogenetic analysis. Based on comparative 16S rRNA gene sequence analysis, strain KMM 9031T constituted a separate phylogenetic line within the Roseobacter clade of the class Alphaproteobacteria, sharing highest sequence similarities with members of the genera Roseovarius (92.7–95.3 %), Pseudoruegeria (94.5 %), Sulfitobacter (92.7–94.4 %) and Thalassobacter (94.2–94.3 %). The predominant fatty acid of strain KMM 9031T was C18 : 1ω7c, with C16 : 0, C10 : 0 3-OH and C12 : 1 3-OH present in lesser amounts. The DNA G+C content of the isolate was 52.6 mol%. The major isoprenoid quinone was Q-10 and polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and two unknown lipids. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KMM 9031T represents a novel species in a new genus, for which the name Pacificibacter maritimus gen. nov., sp. nov. is proposed; the type strain is KMM 9031T ( = NRIC 0785T  = JCM 17096T).

scholarly journals Arthrobacter equi sp. nov., isolated from veterinary clinical material

2011 ◽  
Vol 61 (9) ◽  
pp. 2089-2094 ◽  
Author(s):  
A. F. Yassin ◽  
C. Spröer ◽  
C. Siering ◽  
H. Hupfer ◽  
P. Schumann
Keyword(s):  
Biochemical Characterization ◽  
Rrna Gene ◽  
Positive Staining ◽  
Closely Related Species ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-positive-staining, catalase-positive, non-spore-forming, rod-shaped bacterium, strain IMMIB L-1606T, isolated from genital swabs of a horse, was characterized using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the organism was related to members of the genus Arthrobacter, displaying sequence similarities of 93.5–99.1 % with the type strains of recognized species of the genus. Cell-wall analysis revealed peptidoglycan type A3α l-Lys–l-Ser–l-Thr–l-Ala. DNA–DNA hybridization data and biochemical characterization of strain IMMIB L-1606T enabled the isolate to be differentiated genotypically and phenotypically from phylogenetically closely related species of the genus Arthrobacter. Therefore, it is concluded that strain IMMIB L-1606T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter equi sp. nov. is proposed. The type strain of Arthrobacter equi sp. nov. is IMMIB L-1606T ( = DSM 23395T = CCUG 59597T).

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

scholarly journals Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment

2010 ◽  
Vol 60 (8) ◽  
pp. 1832-1836 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova ◽  
Valery V. Mikhailov
Keyword(s):  
Sequence Similarity ◽  
Phospholipid Fatty Acid ◽  
Fatty Acid Analysis ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Phylogenetic Distance ◽  
Separate Branch ◽  
Novel Genus And Species ◽  
Bacterium Strain

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1 ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1 ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).

scholarly journals Nitritalea halalkaliphila gen. nov., sp. nov., an alkaliphilic bacterium of the family ‘Cyclobacteriaceae’, phylum Bacteroidetes

2010 ◽  
Vol 60 (10) ◽  
pp. 2320-2325 ◽  
Author(s):  
P. Anil Kumar ◽  
T. N. R. Srinivas ◽  
P. Pavan Kumar ◽  
S. Madhu ◽  
S. Shivaji
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
New Genus And Species ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Lonar Lake ◽  
Alkaliphilic Bacterium ◽  
Sequence Similarities

A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7T, was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids were dominated by large amounts of iso-C15 : 0 (59.6 %) and iso-C17 : 0 3-OH (8.9 %). Strain LW7T contained MK-4 and MK-5 as the major respiratory quinones and phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. 16S rRNA gene sequence analysis indicated that Belliella baltica, a member of family ‘Cyclobacteriaceae’ (phylum Bacteroidetes), is the closest related species, with a sequence similarity of 94.0 % to the type strain. Other members of the family ‘Cyclobacteriaceae’ had sequence similarities of <93.3 %. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain LW7T is proposed as a representative of a new genus and species, Nitritalea halalkaliphila gen. nov., sp. nov. The type strain of Nitritalea halalkaliphila is LW7T (=CCUG 57665T =JCM 15946T =NCCB 100279T). The genomic DNA G+C of strain LW7T is 49 mol%.

scholarly journals Thermomonas koreensis sp. nov., a mesophilic bacterium isolated from a ginseng field

2006 ◽  
Vol 56 (7) ◽  
pp. 1615-1619 ◽  
Author(s):  
Myung Kyum Kim ◽  
Wan-Taek Im ◽  
Jun-Gyo In ◽  
Sung-Hoon Kim ◽  
Deok-Chun Yang
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Mesophilic Bacterium ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A Gram-negative, non-spore-forming, rod-shaped, motile bacterium, strain Ko06T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Ko06T belongs to the Gammaproteobacteria, and the highest levels of sequence similarity were with Thermomonas brevis LMG 21746T (98.4 %), Thermomonas fusca LMG 21737T (97.7 %), Thermomonas haemolytica A50-7-3T (96.5 %) and Thermomonas hydrothermalis SGM-6T (95.8 %). Chemotaxonomic data revealed that strain Ko06T possesses ubiquinone Q-8 and that the predominant fatty acids are C15 : 0 iso, C11 : 0 iso and C11 : 0 iso 3-OH, all of which corroborated assignment of the strain to the genus Thermomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Ko06T represents a distinct species. On the basis of these data, strain Ko06T (=KCTC 12540T=NBRC 101155T) should be classified as the type strain of a novel Thermomonas species, for which the name Thermomonas koreensis sp. nov. is proposed.

Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort

2011 ◽  
Vol 61 (4) ◽  
pp. 870-876 ◽  
Author(s):  
S. Schauer ◽  
P. Kämpfer ◽  
S. Wellner ◽  
C. Spröer ◽  
U. Kutschera
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Marchantia Polymorpha ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1T, was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27T, Methylobacterium fujisawaense DSM 5686T, Methylobacterium radiotolerans JCM 2831T and Methylobacterium jeotgali S2R03-9T, with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA–DNA relatedness between strain JT1T and these and the type strains of other closely related species were lower than 70 %. Cells of JT1T stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm−2). Major fatty acids were C18 : 1ω7c and C16 : 0. Based on the morphological, physiological and biochemical data presented, strain JT1T is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1T ( = DSM 21328T  = CCUG 56108T).

scholarly journals Variovorax soli sp. nov., isolated from greenhouse soil

2006 ◽  
Vol 56 (12) ◽  
pp. 2899-2901 ◽  
Author(s):  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Seung-Hee Yoo ◽  
Seon-Young Lee ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Greenhouse Soil ◽  
Variovorax Paradoxus ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Sequence Similarities

A Gram-negative, rod-shaped, non-spore-forming bacterium, strain GH9-3T, isolated from greenhouse soil, was investigated in a polyphasic study. The novel organism grew at 10–35 °C, 0–3 % NaCl and pH 5–9. It had ubiquinone 8 (Q-8) as the predominant isoprenoid quinone and possessed C16 : 0, summed feature 3, C17 : 0 cyclo and C18 : 1 ω7c as the major fatty acids (together representing 87.4 % of the total). The DNA G+C content was 67.1 mol%. 16S rRNA gene sequence analysis of strain GH9-3T showed that it grouped within the Variovorax cluster, with highest sequence similarities to Variovorax paradoxus IAM 12373T (98.3 %) and Variovorax dokdonensis DS-43T (98.0 %). DNA–DNA hybridization values between strain GH9-3T and V. paradoxus DSM 30034T and V. dokdonensis DS-43T were 38 and 29 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic features, it is proposed that strain GH9-3T represents a novel species of the genus Variovorax with the name Variovorax soli sp. nov. The type strain is GH9-3T (=KACC 11579T=DSM 18216T).

scholarly journals Virgibacillus soli sp. nov., isolated from mountain soil

2011 ◽  
Vol 61 (2) ◽  
pp. 275-280 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
H.-J. Busse ◽  
S. Langer ◽  
C.-C. Young ◽  
...  
Keyword(s):  
Rrna Gene ◽  
Positive Bacterium ◽  
Biochemical Tests ◽  
Unidentified Phospholipid ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Physiological And Biochemical

A Gram-positive bacterium (strain CC-YMP-6T) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6T clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6T were iso-C15 : 0 and anteiso-C15 : 0. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6T from all recognized species of the genus Virgibacillus. Strain CC-YMP-6T is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6T (=DSM 22952T=CCM 7714T).

scholarly journals Pseudonocardia oroxyli sp. nov., a novel actinomycete isolated from surface-sterilized Oroxylum indicum root

2006 ◽  
Vol 56 (9) ◽  
pp. 2193-2197 ◽  
Author(s):  
Qiang Gu ◽  
Hongli Luo ◽  
Wen Zheng ◽  
Zhiheng Liu ◽  
Ying Huang
Keyword(s):  
Dna Hybridization ◽  
Rrna Gene ◽  
Positive Bacterium ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Oroxylum Indicum ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Physiological And Biochemical ◽  
Chinese Medicinal Plant

A high-G+C-content, Gram-positive bacterium, strain D10T, was isolated from the root of Oroxylum indicum, a Chinese medicinal plant. Based on 16S rRNA gene sequence analysis, strain D10T was a member of the genus Pseudonocardia and was most closely related, albeit loosely, to Pseudonocardia halophobica. Morphological and chemotaxonomic characteristics support the affiliation of strain D10T to the genus Pseudonocardia. Results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain D10T from related Pseudonocardia species. Strain D10T (=CGMCC 4.3143T=DSM 44984T) therefore represents a novel species, for which the name Pseudonocardia oroxyli sp. nov. is proposed.

scholarly journals Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier

2006 ◽  
Vol 56 (12) ◽  
pp. 2921-2925 ◽  
Author(s):  
De-Chao Zhang ◽  
He-Xiang Wang ◽  
Hong-Can Liu ◽  
Xiu-Zhu Dong ◽  
Pei-Jin Zhou
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Psychrophilic Bacterium ◽  
Obligate Aerobic ◽  
Bacterium Strain ◽  
The Common ◽  
Sequence Similarities

A novel psychrophilic, yellow-pigmented and obligate aerobic bacterium, strain 0499T, was isolated from the China No.1 glacier. Strain 0499T displayed the common phenotypic and chemotaxonomic features of the genus Flavobacterium, containing menaquinone-6 (MK-6) as the major quinone and C15 : 0, iso-C15 : 0, C17 : 1 ω6c and summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH) as the major fatty acids. Optimal growth occurred at 21 °C. The genomic DNA G+C content was 36.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain 0499T was related to members of the genus Flavobacterium, sharing the highest sequence similarities with Flavobacterium succinicans (97.9 %), Flavobacterium granuli (97.4 %) and Flavobacterium hydatis (97.2 %). On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species Flavobacterium glaciei is proposed with strain 0499T (=CGMCC 1.5380T=JCM 13953T) as the type strain.

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