scholarly journals Six novel Arthrobacter species isolated from deteriorated mural paintings

2005 ◽  
Vol 55 (4) ◽  
pp. 1457-1464 ◽  
Author(s):  
Jeroen Heyrman ◽  
Jens Verbeeren ◽  
Peter Schumann ◽  
Jean Swings ◽  
Paul De Vos
Keyword(s):  
Biofilm Formation ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Mural Paintings ◽  
Dna Base ◽  
Gene Sequence Analysis ◽  
Respective Type ◽  
Arthrobacter Species ◽  
Type Strains

A group of 21 bacterial strains was isolated from samples of biofilm formation in the Servilia tomb (necropolis of Carmona, Spain) and the Saint-Catherine chapel (castle at Herberstein, Austria). A polyphasic taxonomic study of these isolates, including morphological, biochemical and chemotaxonomic characterization, rep-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA base ratio and DNA–DNA relatedness studies, allocated them to the genus Arthrobacter. The isolates represent six novel species, for which the names Arthrobacter castelli sp. nov., Arthrobacter monumenti sp. nov., Arthrobacter parietis sp. nov., Arthrobacter pigmenti sp. nov., Arthrobacter tecti sp. nov. and Arthrobacter tumbae sp. nov. are proposed. The respective type strains are LMG 22283T (=DSM 16402T), LMG 19502T (=DSM 16405T), LMG 22281T (=DSM 16404T), LMG 22284T (=DSM 16403T), LMG 22282T (=DSM 16407T) and LMG 19501T (=DSM 16406T).

scholarly journals Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil

2007 ◽  
Vol 57 (7) ◽  
pp. 1594-1598 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Myung-Hee Song ◽  
Jung-A Son ◽  
Byung-Yong Kim ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Rrna Gene ◽  
Flavobacterium Columnare ◽  
Bacterial Strains ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Greenhouse Soils ◽  
Type Strains ◽  
Flavobacterium Aquatile ◽  
Sequence Similarities

Two bacterial strains, R2A1-13T and R2A45-3T, were isolated from greenhouse soils in Korea. The cells of both strains were Gram-negative, aerobic and rod-shaped. 16S rRNA gene sequence analysis placed the isolates in the genus Flavobacterium within the family Flavobacteriaceae. Strain R2A1-13T was found to be related to Flavobacterium columnare IAM 14301T, Flavobacterium saliperosum CGMCC1.3801T and Flavobacterium croceum EMB47T, with sequence similarities of 96.8, 95.0 and 94.6 %, respectively. Strain R2A45-3T was found to be related to F. croceum EMB47T and Flavobacterium aquatile ATCC 11947T, with sequence similarities of 94.7 and 94.6 %, respectively. Both strains contained iso-C15 : 0 and iso-C16 : 0 as the main fatty acids and contained a menaquinone with six isoprene units (MK-6) as the major isoprenoid quinone. The G+C contents of the DNA from strains R2A1-13T and R2A45-3T were 34 and 38 mol%, respectively. A polyphasic taxonomic study revealed that these strains belong to two novel species within the genus Flavobacterium, for which the names Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov. are proposed. The type strains of F. terrae sp. nov. and F. cucumis sp. nov. are R2A1-13T (=KACC 11731T=DSM 18829T) and R2A45-3T (=KACC 11732T=DSM 18830T), respectively.

scholarly journals Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil

2011 ◽  
Vol 61 (4) ◽  
pp. 979-984 ◽  
Author(s):  
Lars Ganzert ◽  
Felizitas Bajerski ◽  
Kai Mangelsdorf ◽  
André Lipski ◽  
Dirk Wagner
Keyword(s):  
Type Strain ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Cold Tolerant ◽  
Respective Type ◽  
Ph Range ◽  
Type Strains ◽  
Physiological And Biochemical

Two novel cold-tolerant, Gram-stain-positive, motile, facultatively anaerobic bacterial strains, LI2T and LI3T, were isolated from moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St Kliment Ohridski. A rod–coccus cycle was observed for both strains. 16S rRNA gene sequence analysis revealed an affiliation to the genus Arthrobacter, with the highest similarity to Arthrobacter stackebrandtii and Arthrobacter psychrochitiniphilus for strain LI2T (97.8 and 97.7 % similarity to the respective type strains) and to Arthrobacter kerguelensis and Arthrobacter psychrophenolicus for strain LI3T (97.4 and 97.3 % similarity to the respective type strains). The growth temperature range was −6 to 28 °C for LI2T and −6 to 24 °C for LI3T, with an optimum at 16 °C for both strains. Growth occurred at 0–10 % (w/v) NaCl, with optimum growth at 0–1 % (w/v) for LI2T and 0.5–3 % (w/v) for LI3T. The pH range for growth was pH 4–9.5 with an optimum of pH 8 for LI2T and pH 6.5 for LI3T. The predominant fatty acids were anteiso-C15 : 0, C18 : 0 and anteiso-C17 : 0 for LI2T and anteiso-C15 : 0 and C18 : 0 for LI3T. Physiological and biochemical tests clearly differentiated strain LI2T from A. stackebrandtii and A. psychrochitiniphilus and strain LI3T from A. kerguelensis and A. psychrophenolicus. Therefore, two novel species within the genus Arthrobacter are proposed: Arthrobacter livingstonensis sp. nov. (type strain LI2T  = DSM 22825T  = NCCB 100314T) and Arthrobacter cryotolerans sp. nov. (type strain LI3T  = DSM 22826T  = NCCB 100315T).

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 Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan

2004 ◽  
Vol 54 (6) ◽  
pp. 1927-1931 ◽  
Author(s):  
Akiko Kageyama ◽  
Katsukiyo Yazawa ◽  
Akira Mukai ◽  
Mari Kinoshita ◽  
Nobukatsu Takata ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Morphological Criteria ◽  
Respective Type ◽  
Type Strains

Three actinomycete strains isolated from soils and one strain isolated from a patient with lung nocardiosis in 1999 and 2001 in Japan have been provisionally assigned to the genus Nocardia on the basis of morphological criteria. These isolates were further investigated to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rRNA gene sequence analysis of these isolates confirmed that they belong to the genus Nocardia. The 16S rRNA gene sequences of the four strains were most similar to that of Nocardia farcinica. However, the sequence similarity values between these four strains and N. farcinica were <98·9 %. These four strains were susceptible to 5-fluorouracil, and they have the ability to decompose urea, which is a very characteristic trait. Furthermore, DNA–DNA relatedness data revealed that IFM 10311T, IFM 10312 and IFM 10313 comprise a single novel species of Nocardia, that IFM 10084T represents another novel species of Nocardia and that these two novel species could be distinguished from N. farcinica. The names Nocardia shimofusensis sp. nov. and Nocardia higoensis sp. nov. are proposed, with IFM 10311T (=NBRC 100134T=JCM 12122T=DSM 44733T) and IFM 10084T (=NBRC 100133T=JCM 12121T=DSM 44732T) as the respective type strains.

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

scholarly journals Halomonas daqiaonensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from a littoral saltern

2011 ◽  
Vol 61 (7) ◽  
pp. 1612-1616 ◽  
Author(s):  
Lingyun Qu ◽  
Qiliang Lai ◽  
Fengling Zhu ◽  
Xuguang Hong ◽  
Jinxing Zhang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
East Coast ◽  
Novel Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis

Two novel Gram-negative, oxidase- and catalase-positive, rod-shaped bacterial strains, designated YCSA28T and YCSA39, were isolated from sediment of Daqiao saltern, Jimo, Qingdao, on the east coast of China. The two strains grew optimally at 28–30 °C, at pH 7.5 and in the presence of 7–8 % (w/v) NaCl. They were assigned to the genus Halomonas, class Gammaproteobacteria, based on 16S rRNA gene sequence analysis. The major cellular fatty acids of the two strains were C18 : 1ω7c (42.9 %), C16 : 0 (23.1 %) and C16 : 1ω7c/ω6c (18.0 %), and Q-9 was the major ubiquinone. The G+C content of the DNA of strains YCSA28T and YCSA39 was 63.7 and 63.9 mol%, respectively. The predominant respiratory lipoquinone, cellular fatty acid profiles and DNA G+C content of strains YCSA28T and YCSA39 were consistent with those of recognized species of the genus Halomonas. Levels of DNA–DNA relatedness between strains YCSA28T and YCSA39, between YCSA28T and Halomonas ventosae Al12T, and between YCSA39 and H. ventosae Al12T were 95, 45 and 50 %, respectively. Together, these data indicated that strains YCSA28T and YCSA39 represent a single novel species of the genus Halomonas, for which the name Halomonas daqiaonensis sp. nov. is proposed. The type strain is YCSA28T ( = CGMCC 1.9150T  = NCCB 100305T  = MCCC 1B00920T).

Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete

2011 ◽  
Vol 61 (3) ◽  
pp. 482-486 ◽  
Author(s):  
Sung M. Kim ◽  
Sae W. Park ◽  
Sang T. Park ◽  
Young M. Kim
Keyword(s):  
Carbon Monoxide ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).

scholarly journals Marichromatium fluminis sp. nov., a slightly alkaliphilic, phototrophic gammaproteobacterium isolated from river sediment

2010 ◽  
Vol 60 (5) ◽  
pp. 1103-1107 ◽  
Author(s):  
K. Sucharita ◽  
E. Shiva Kumar ◽  
Ch. Sasikala ◽  
B. B. Panda ◽  
S. Takaichi ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Base Composition ◽  
Dna Base ◽  
Gene Sequence Analysis

An anoxygenic, phototrophic gammaproteobacterium designated strain JA418T was isolated from a sediment sample collected from the Baitarani River, Orissa, India. The bacterium was a Gram-negative, motile rod with a single polar flagellum. Bacteriochlorophyll a and rhodopin were the major photosynthetic pigments. The organism grew best at slightly alkaline pH (8–8.5) and lacked chemotrophic growth. The major fatty acids were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA418T clusters with species of the genus Marichromatium belonging to the class Gammaproteobacteria. The highest 16S rRNA gene sequence similarities of strain JA418T were found with the type strains of Marichromatium gracile (95.9 %), Marichromatium indicum (95.6 %), Marichromatium purpuratum (95.5 %) and Marichromatium bheemlicum (95.6 %). The DNA base composition of strain JA418T was 71.4 mol% G+C (by HPLC). Based on the 16S rRNA gene sequence analysis and physiological and chemotaxonomic characteristics, strain JA418T is sufficiently different from other Marichromatium species to merit the description of a novel species, Marichromatium fluminis sp. nov., to accommodate it. The type strain is JA418T (=KCTC 5717T =NBRC 105221T).

Paracoccus caeni sp. nov., isolated from sludge

2011 ◽  
Vol 61 (8) ◽  
pp. 1968-1972 ◽  
Author(s):  
Myungjin Lee ◽  
Song-Geun Woo ◽  
Giho Park ◽  
Myung Kyum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, non-motile bacterium, designated MJ17T, was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17T belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17T and type strains of species of the genus Paracoccus were 94.1–97.4 %. The highest similarities were between strain MJ17T and Paracoccus homiensis DD-R11T, Paracoccus zeaxanthinifaciens ATCC 21588T and Paracoccus alcaliphilus JCM 7364T (97.4, 97.2 and 96.3 %, respectively). Strain MJ17T exhibited <22 % DNA–DNA relatedness with P. homiensis KACC 11518T and P. zeaxanthinifaciens JCM 21774T. The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17T contained ubiquinone Q-10. The major fatty acids were C18 : 0 (11.3 %), C16 : 0 (10.2 %) and summed feature 7 (containing one or more of C18 : 1ω7c, C18 : 1ω9c and C18 : 1ω12t; 54.3 %). Poly-β-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17T ( = KCTC 22480T  = JCM 16385T  = KEMB 9004-001T).

scholarly journals Marinomonas ostreistagni sp. nov., isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China

2006 ◽  
Vol 56 (10) ◽  
pp. 2271-2275 ◽  
Author(s):  
Ken W. K. Lau ◽  
Jianping Ren ◽  
Natalie L. M. Wai ◽  
Simon C. L. Lau ◽  
Pei-Yuan Qian ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Pearl Oyster ◽  
Rrna Gene ◽  
Hainan Province ◽  
Oyster Culture ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-negative, aerobic, halophilic, neutrophilic, rod-shaped, non-pigmented, polar-flagellated bacterium, UST010306-043T, was isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China in January 2001. This marine bacterium had an optimum temperature for growth of between 33 and 37 °C. On the basis of 16S rRNA gene sequence analysis, the strain was closely related to Marinomonas aquimarina and Marinomonas communis, with 97.5–97.7 and 97.1 % sequence similarity, respectively. Levels of DNA–DNA relatedness to the type strains of these species were well below 70 %. Analyses of phylogenetic, phenotypic and chemotaxomonic characteristics showed that strain UST010306-043T was distinct from currently established Marinomonas species. A novel species with the name Marinomonas ostreistagni sp. nov. is proposed to accommodate this bacterium, with strain UST010306-043T (=JCM 13672T=NRRL B-41433T) as the type strain.

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