scholarly journals Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 327-331 ◽  
Author(s):  
Ju-Hee Cha ◽  
Chang-Jun Cha
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment ◽  
Gene Sequence Analysis

A Gram-stain-positive, non-motile, aerobic actinobacterium, designated strain CJ10T, was isolated from tidal flat sediment from the Yellow Sea in South Korea. Strain CJ10T grew on tryptic soy agar in the presence of 0–4 % (w/v) NaCl (optimum growth in the absence of NaCl) and at pH 6–11 (optimum pH 9). On the basis of 16S rRNA gene sequence analysis, strain CJ10T belonged to the genus Gordonia and showed the highest sequence similarity to Gordonia hirsuta DSM 44140T (97.9 %) and Gordonia hydrophobica DSM 44015T (97.6 %). DNA–DNA relatedness levels of strain CJ10T were 47.4 % (CJ10T as probe) and 42.2 % ( G. hirsuta DSM 44140T as probe) to G. hirsuta DSM 44140T and 8.6 % (CJ10T as probe) and 9.3 % ( G. hydrophobica DSM 44015T as probe) to G. hydrophobica DSM 44015T. The major isoprenoid quinone was MK-9(H2). The polar lipid profile of strain CJ10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were C18 : 1ω9c (38.0 %), C16 : 0 (30.1 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 17.4 %). The DNA G+C content was 67.7 mol%. Therefore, the results from our polyphasic taxonomic study suggest that strain CJ10T represents a novel species in the genus Gordonia , for which the name Gordonia alkaliphila sp. nov. is proposed; the type strain is CJ10T ( = KACC 16561T  = JCM 18077T).

scholarly journals Erythrobacter lutimaris sp. nov., isolated from a tidal flat sediment

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4184-4190 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-motile, coccoid- or oval-shaped bacterial strain, designated S-5T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea and was subjected to a polyphasic taxonomic study. Strain S-5T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining analysis based on 16S rRNA gene sequences showed that strain S-5T fell within the clade comprising the species of the genus Erythrobacter , clustering with the type strains of Erythrobacter pelagi , Erythrobacter citreus and Erythrobacter seohaensis with which it exhibited the highest 16S rRNA gene sequence similarity (96.0–96.7 %). The DNA G+C content was 66.0 mol%. Strain S-5T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-5T is distinguishable from other species of the genus Erythrobacter . On the basis of the data presented, strain S-5T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter lutimaris sp. nov. is proposed. The type strain is S-5T ( = KCTC 42109T = CECT 8624T).

Ferrimonas gelatinilytica sp. nov., isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4309-4314 ◽  
Author(s):  
Mohammad Mizanur Rahman ◽  
Chang-Jun Cha
Keyword(s):  
16S Rrna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Anaerobic Bacteria ◽  
Minor Component ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A novel beige-pigmented, Gram-staining-negative, coccoid, motile and facultatively anaerobic bacteria, designated strain CJ24T, was isolated from the tidal flat sediment of the Yellow Sea in South Korea. Characterization of this strain was performed on the basis of polyphasic taxonomic methods. Phylogenetic analysis of the 16S rRNA and gyrB genes revealed that strain CJ24T belongs to the genus Ferrimonas , sharing the highest 16S rRNA gene sequence similarity of 96.9 % with Ferrimonas marina DSM 16917T. Strain CJ24T was able to grow optimally at 30 °C, at pH 6.0 and in the presence of 2 % NaCl (w/v). As an isoprenoid quinone, menaquinone (MK-7) was predominantly identified from this strain, while ubiquinone (Q-7) was also present as a minor component. The DNA G+C content of strain CJ24T was 60.2 mol%. The most abundant cellular fatty acids were C15 : 0 iso, C18 : 1ω9c, C16 : 0 and C17 : 0 iso. Therefore, strain CJ24T represents a novel species in the genus Ferrimonas for which the name Ferrimonas gelatinilytica sp. nov. is proposed; the type strain is CJ24T ( = KACC 17065T = JCM 18720T).

Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1001-1006 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strain, BB-Mw22T, was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30–37 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22T belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22T was clearly separated from other taxa. Strain BB-Mw22T exhibited 95.3–98.7 % 16S rRNA gene sequence similarity to the type strains of recognized Kangiella species. Strain BB-Mw22T contained Q-8 as the predominant ubiquionone and iso-C15 : 0 and iso-C11 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22T was 48.9 mol%, and its mean DNA–DNA hybridization values with Kangiella geojedonensis YCS-5T, Kangiella japonica JCM 16211T and Kangiella taiwanensis JCM 17727T were 14–28 %. Phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22T is distinguishable from all recognized Kangiella species. On the basis of the data presented, strain BB-Mw22T is considered to represent a novel species of the genus Kangiella , for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22T ( = KCTC 23892T  = CCUG 62217T).

Brumimicrobium mesophilum sp. nov., isolated from a tidal flat sediment, and emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1105-1110 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Hyun-Myung Oh ◽  
Sang-Jin Kim ◽  
Jung-Hyun Lee ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Major Respiratory Quinone

A Gram-stain-negative, aerobic, rod-shaped, non-motile and orange-coloured marine bacterium, YH207T, was isolated from a tidal flat at Yeongheung-do on the coast of the Yellow Sea, Korea. 16S rRNA gene sequence analysis revealed that strain YH207T was affiliated with the family Cryomorphaceae and showed highest similarity to Brumimicrobium glaciale IC156T (95.4 %). Growth was observed at 11–36 °C, at pH 6.5–10.0 and with 0.4–7.0 % NaCl. The predominant cellular fatty acids when grown at 20 °C were iso-C15 : 0 (44.2 %), iso-C15 : 1 G (34.3 %), iso-C17 : 0 3-OH (8.7 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c; 2.3 %). The major respiratory quinone was MK-6. Phosphatidylethanolamine, phosphatidylglycerol, three unidentified lipids, three unidentified aminophospholipids, one unidentified phospholipid, four unidentified aminolipids and three unidentified glycolipids were identified as major polar lipids. The DNA G+C content was 34.3 mol%. On the basis of the data from our polyphasic taxonomic study, strain YH207T should be classified in a novel species in the genus Brumimicrobium , for which the name Brumimicrobium mesophilum sp. nov. is proposed. The type strain is YH207T ( = KCCM 42331T  = JCM 14063T). Emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale Bowman et al. 2003 are also given.

Chitinophaga taiwanensis sp. nov., isolated from the rhizosphere of Arabidopsis thaliana

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 426-430 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
Wei-An Lai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

An aerobic, Gram-stain-negative, rod-shaped bacterium (strain CC-ALB-1T) was isolated from the rhizosphere of Arabidopsis thaliana. Strain CC-ALB-1T was able to grow at 20–30 °C, pH 5.0–8.0 and with up to 1.0 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain CC-ALB-1T had the highest sequence similarity to Chitinophaga ginsengisegetis Gsoil 040T (96.9 %) and Chitinophaga niastensis JS16-4T (96.7 %); lower levels of similarity (<97.0 %) were observed to strains of all other species of the genus Chitinophaga . The fatty acid profile consisted of iso-C15 : 0, iso-C17 : 0 3-OH, C15 : 1ω5c, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant quinone system was menaquinone 7 (MK-7). The DNA G+C content was 53.4±0.4 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-1T is proposed to represent a novel species within the genus Chitinophaga , for which the name Chitinophaga taiwanensis sp. nov. is proposed. The type strain is CC-ALB-1T ( = BCRC 80570T = JCM 18895T).

scholarly journals Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 2969-2974 ◽  
Author(s):  
Sooyeon Park ◽  
Sung-Min Won ◽  
Hyangmi Kim ◽  
Doo-Sang Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, BS-B2T, which was isolated from a tidal flat sediment at Boseong in South Korea, was characterized taxonomically. Strain BS-B2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The novel strain exhibited highest 16S rRNA gene sequence similarity (97.4 %) to Marivita geojedonensis DPG-138T. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain BS-B2T is closely related to Primorskyibacter sedentarius KMM 9018T, showing 96.5 % sequence similarity. Strain BS-B2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain BS-B2T comprised phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, and differentiated it from the type strains of P. sedentarius and M. geojedonensis . The DNA G+C content of strain BS-B2T was 62.2 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain BS-B2T can be distinguished from phylogenetically related genera as well as P. sedentarius and M. geojedonensis . On the basis of the data presented, strain BS-B2T is considered to represent a novel species of a new genus, for which the name Aestuariivita boseongensis gen. nov., sp. nov. is proposed. The type strain of Aestuariivita boseongensis is BS-B2T ( = KCTC 42052T = CECT 8532T).

scholarly journals Paracoccus sediminilitoris sp. nov., isolated from a tidal flat sediment

2019 ◽  
Vol 69 (4) ◽  
pp. 1035-1040 ◽  
Author(s):  
Yuli Wei ◽  
Junwei Cao ◽  
Huimin Yao ◽  
Haiyan Mao ◽  
Kelei Zhu ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A novel marine Gram-stain-negative, non-spore-forming, motile, aerobic, coccoid or ovoid bacterium, designated as strain DSL-16T, was isolated from a tidal flat sediment on the East China Sea and characterized phylogenetically and phenotypically. Optimal growth of the strain occurred at 35 °C (range 4–40 °C), at pH 6 (range 5–11) and with 4 % (w/v) NaCl (range 1–14 %). The nearest phylogenetic neighbour was Paracoccus seriniphilus DSM 14827T (98.2 % 16S rRNA gene sequence similarity). The digital DNA–DNA hybridization value between strain DSL-16T and P. seriniphilus DSM 14827T was 19.5±2.2 %. The average nucleotide identity value between strain DSL-16T and P. seriniphilus DSM 14827T was 83.6 %. The sole respiratory ubiquinone was Q-10. The major polar lipids were phosphatidylmonomethylethanolamine (PME), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidyglycerol (DPG) and glycolipid (GL). The predominant cellular fatty acids of strain DSL-16T were C18 : 1ω7c, C18 : 0 and 11-methyl C18 : 1ω7c. The G+C content of the genomic DNA was 64.5 mol%. The combined genotypic and phenotypic data indicated that strain DSL-16T represents a novel species of the genus Paracoccus , for which the name Paracoccus sediminilitoris sp. nov. is proposed. The type strain is DSL-16T (=KCTC 62644T=MCCC 1K03534T).

Algoriphagus chungangensis sp. nov., isolated from a tidal flat sediment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 648-653 ◽  
Author(s):  
Hyeonji Kang ◽  
Veeraya Weerawongwiwat ◽  
Min Young Jung ◽  
Soon Chul Myung ◽  
Wonyong Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated CAU 1002T, was isolated from a tidal flat sediment and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1002T grew optimally at 30 °C and pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1002T formed a distinct lineage within the genus Algoriphagus and was most closely related to Algoriphagus lutimaris KCTC 22630T and Algoriphagus halophilus KCTC 12051T (97.75 and 97.74 % 16S rRNA gene sequence similarity, respectively). The strain contained MK-7 as the major isoprenoid quinone and iso-C15 : 0 and C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3) as the major fatty acids. The cell-wall peptidoglycan of strain CAU 1002T contained meso-diaminopimelic acids. The major whole-cell sugars were glucose, arabinose, sucrose, and ribose. The polar lipid profile was composed of phosphatidylethanolamine, five unidentified aminolipids, one unidentified aminophospholipid, one unidentified phospholipid, one unidentified aminoglycolipid, one unidentified glycolipid and twelve unidentified lipids. The DNA G+C content of strain CAU 1002T was 38.0 mol%. On the basis of phylogenetic inference, phenotypic, chemotaxonomic and genotypic data, strain CAU 1002T should be classified into the genus Algoriphagus as a member of a novel species, for which the name Algoriphagus chungangensis sp. nov. is proposed. The type strain is CAU 1002T ( = KCTC 23759T = CCUG 61890T). The description of the genus Algoriphagus is emended.

scholarly journals Salinimicrobium gaetbulicola sp. nov., isolated from tidal flat sediment

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1027-1031 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, aerobic, non-flagellated, non-gliding and short rod- or rod-shaped bacterial strain, designated BB-My20T, was isolated from tidal flat sediment taken from the southern coast of Korea. Strain BB-My20T grew optimally at 37 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed that strain BB-My20T fell within the clade comprising Salinimicrobium species, joining Salinimicrobium catena HY1T, with which it had a 16S rRNA gene sequence similarity value of 97.4 %. It exhibited 95.4–96.9 % sequence similarity to the type strains of other members of the genus Salinimicrobium . Strain BB-My20T contained MK-6 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain BB-My20T and S. catena JCM 14015T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain BB-My20T was 45.1 mol% and its mean DNA–DNA relatedness value with S. catena JCM 14015T was 4.5 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain BB-My20T can be distinguished from the four recognized species of the genus Salinimicrobium . On the basis of the data presented, strain BB-My20T is considered to represent a novel species of the genus Salinimicrobium , for which the name Salinimicrobium gaetbulicola sp. nov. is proposed; the type strain is BB-My20T ( = KCTC 23579T = CCUG 60898T).

Lutibacter flavus sp. nov., a marine bacterium isolated from a tidal flat sediment

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 946-951 ◽  
Author(s):  
Ahyoung Choi ◽  
Seung-Jo Yang ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A carotenoid-containing chemoheterotrophic bacterium, designated IMCC1507T, was isolated from a tidal flat sediment of the Yellow Sea, Korea. Strain IMCC1507T was Gram-negative, yellow, obligately aerobic, non-motile and flexirubin-negative. 16S rRNA gene sequence analysis indicated that strain IMCC1507T belonged to the genus Lutibacter in the family Flavobacteriaceae and exhibited 96.1–97.3 % 16S rRNA sequence similarity with the type strains of described species of the genus Lutibacter . DNA–DNA relatedness between strain IMCC1507T and Lutibacter litoralis KCCM 42118T ranged from 3.5±2.2 % to 11.2±2.4 %, indicating that strain IMCC1507T represented a novel genomic species in the genus Lutibacter . Chemotaxonomic characteristics of the isolate, i.e. the DNA G+C content (31.4 mol%), iso-C15 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0 as the major fatty acids, MK-6 as the predominant menaquinone and phosphatidylethanolamine as the major polar lipid, were consistent with its assignment to the genus Lutibacter . However, several phenotypic characteristics, including hydrolysis of macromolecules, enzyme activities and carbon source oxidation, differentiated strain IMCC1507T from members of the genus. Data from this study indicate that strain IMCC1507T represents a novel species in the genus Lutibacter , for which the name Lutibacter flavus sp. nov. is proposed. The type strain is IMCC1507T ( = KACC 14312T  = NBRC 107589T).

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