Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 481-486 ◽  
Author(s):  
Christian Suarez ◽  
Stefan Ratering ◽  
Irina Kramer ◽  
Sylvia Schnell
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Content Sharing ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Salt Meadow ◽  
The 16S Rrna Gene

Two Gram-reaction-negative, aerobic, nitrogen-fixing, rod-shaped bacteria, designated strains E20 and E50T, were isolated from the rhizosphere of salt meadow plants Plantago winteri and Hordeum secalinum, respectively, near Münzenberg, Germany. Based on the 16S rRNA gene sequence analysis both strains E20 and E50T are affiliated with the genus Cellvibrio , sharing the highest similarity with Cellvibrio gandavensis LMG 18551T (96.4 %) and (97.1 %), respectively. Strains E20 and E50T were oxidase and catalase-positive, grew at a temperature range between 16 and 37 °C and in the presence of 0–5 % NaCl (w/v). The DNA G+C contents were 52.1 mol% (E20) and 51.6 mol% (E50T). Major fatty acids of strains E20 and E50T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C12 : 0, C18 : 0 and C12 : 0 3-OH. The DNA–DNA relatedness of the strains to Cellvibrio gandavensis LMG 18551T was 39 % for strain E20 and 58 % for strain E50T. The nitrogen fixation capability of strains E20 and E50T was confirmed by the acetylene reduction assay. On the basis of our polyphasic taxonomic study, strains E20 and E50T represent a novel species of the genus Cellvibrio , for which the name Cellvibrio diazotrophicus is proposed. The type strain of Cellvibrio diazotrophicus is E50T ( = LMG 27267T = KACC 17069T). An emended description of the genus Cellvibrio is proposed based on the capability of fixing nitrogen and growth in presence of up to 5 % NaCl (w/v).

scholarly journals Kiloniella spongiae sp. nov., isolated from a marine sponge and emended description of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 230-234 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Jung-Hyun Lee ◽  
Sang-Jin Kim ◽  
Kae Kyoung Kwon
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Emended Description ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-negative, aerobic, rod-shaped and non-motile marine bacterium, designated MEBiC09566T was isolated from a sponge collected at Uljin County in the coastal area of the East Sea (36° 55′ N, 129° 25′ E), Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC09566T showed the highest similarity with the Kiloniella laminariae LD81T (96.7 %). Growth was observed at 11–31 °C (optimum 25 °C), at pH 6.0–8.5 (optimum pH 7.0) and with 0–6 % (optimum 2.5 %) NaCl. The predominant cellular fatty acids were summed feature 8 (comprised of C18 : 1ω7c/C18 : 1ω6c) and summed feature 3 (comprised of C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content is 44.6 mol%. The major respiratory quinone is Q-9. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified lipid, two unidentified aminophospholipids and one unidentified aminolipid were detected as major polar lipids. On the basis of this polyphasic taxonomic data, it is concluded that strain MEBiC09566T should be classified as representing a novel species in the genus Kiloniella and the name proposed is Kiloniella spongiae sp. nov. The type strain is MEBiC09566T ( = KCCM 43040T = JCM 19930T). Emended descriptions of the genus Kiloniella Wiese et al. 2009 and Kiloniella laminariae are also given.

scholarly journals Agromyces humi sp. nov., actinobacterium isolated from farm soil

2020 ◽  
Vol 70 (9) ◽  
pp. 5032-5039 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Phyletic Line ◽  
Phylogenomic Analyses ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and at salinities of 0–4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA–DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces . The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 :  0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces , for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).

scholarly journals Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1241-1244 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Single Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Emended Description

Strains of the recently proposed species Bacteroides chinchillae share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of Bacteroides sartorii although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position. B. chinchillae JCM 16497T exhibited high hsp60 gene sequence similarity with B. sartorii JCM 17136T (100 %) as well as B. chinchillae JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA–DNA relatedness observed demonstrated B. sartorii JCM 17136T, B. chinchillae JCM 16497T, and B. chinchillae JCM 16498 are members of a single species. Based on these data, we propose Bacteroides chinchillae as a later heterotypic synonym of Bacteroides sartorii . An emended description of B. sartorii is provided.

Actinoplanes siamensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3037-3042 ◽  
Author(s):  
Chanwit Suriyachadkun ◽  
Wipaporn Ngaemthao ◽  
Suwanee Chunhametha ◽  
Chitti Thawai ◽  
Jean-Jacques Sanglier
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A Gram-positive filamentous bacterial strain that developed large campanulate sporangia at the ends of sporangiophores on substrate mycelium was isolated from bamboo forest soil in Thailand. According to the results of a polyphasic taxonomic study, our isolate had typical characteristics of members of the genus Actinoplanes . The 16S rRNA gene sequence analysis also indicated that strain A-T 6646T belonged to the genus Actinoplanes , being most closely related to Actinoplanes liguriensis DSM 43865T (97.61 %) and Actinoplanes octamycinicus NBRC 14524T (97.52 %). The DNA–DNA relatedness values, which differentiate the new strain from the most closely related species, were significantly below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained xylose and arabinose. The predominant menaquinone was MK-9(H4). The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and anteiso-C15 : 0. Following an evaluation of phenotypic, chemotaxonomic and genotypic studies, the isolate is proposed to represent a novel species to be named Actinoplanes siamensis sp. nov. The type strain is A-T 6646T ( = BCC 46194T = NBRC 109076T).

Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2975-2980 ◽  
Author(s):  
Ngoc-Lan Nguyen ◽  
Yeon-Ju Kim ◽  
Van An Hoang ◽  
Deok-Chun Yang
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Chryseobacterium Gleum

Strain DCY 63T, isolated from the rhizosphere of ginseng, was a Gram-reaction-negative, strictly aerobic, non-motile, catalase- and oxidase-positive rod. 16S rRNA gene sequence analysis revealed that strain DCY 63T belonged to the genus Chryseobacterium and was closely related to Chryseobacterium indoltheticum LMG 4025T (98.1 %), Chryseobacterium ginsenosidimutans THG 15T (98.0 %) and Chryseobacterium scophthalmum LMG 13028T (97.1 %). The major polar lipids of strain DCY 63T were phosphatidylethanolamine (PE), four unidentified aminolipids and three unidentified polar lipids, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The predominant isoprenoid quinone of strain DCY 63T was MK-6 and the G+C content of the genomic DNA was 31.6 mol%. The DNA–DNA relatedness values between strain DCY 63T and C. indoltheticum LMG 4025T, C. ginsenosidimutans THG 15T and C. scophthalmum LMG 13028T were less than 30 %. On the basis of these data, strain DCY 63T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY 63T ( = KCTC 23760T = JCM 18019T). An emended description of Chryseobacterium gleum is also proposed.

scholarly journals Sphingobium paulinellae and Sphingobium algicola Lee and Jeon 2017 are two later heterotypic synonyms of Sphingobium limneticum Chen et al. 2013 and emended description of the species

2020 ◽  
Vol 70 (3) ◽  
pp. 1644-1647 ◽  
Author(s):  
Guang-Da Feng ◽  
Qing-Bai Wang ◽  
Xian-Jiao Zhang ◽  
Wen-Di Chen ◽  
Jia-Li Li ◽  
...  
Keyword(s):  
Type Species ◽  
Species Discrimination ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Close Relationship ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Genomic Relatedness

Phylogenetic analysis of the genus Sphingobium had shown that the type strains of Sphingobium paulinellae , Sphingobium algicola and Sphingobium limneticum shared a very close relationship between each other. The 16S rRNA gene sequences similarity values between each other ranged from 99.65 to 99.93 %. Whole genome sequencing was performed and genomic relatedness values between each pair of the species were 97.49–100 % (ANI) and 79.3–100 % (dDDH), respectively, all higher than the threshold values of 95–96 % ANI and 70 % dDDH suggested for species discrimination, and implicated that the type strains should belong to the same species of the genus Sphingobium . The phenotypic and chemotaxonomic characterizations performed in the original descriptions of S. paulinellae and S. algicola also supported the same conclusion. Due to priority of publication Sphingobium paulinellae and Sphingobium algicola Lee and Jeon 2017, should be taken as two later heterotypic synonyms of Sphingobium limneticum Chen et al. 2013. Correspondingly, the species description of Sphingobium limneticum was emended based on this study.

scholarly journals Skermanella pratensis sp. nov., isolated from meadow soil, and emended description of the genus Skermanella

2020 ◽  
Vol 70 (3) ◽  
pp. 1605-1609 ◽  
Author(s):  
Qiannan Guo ◽  
Zhengfu Zhou ◽  
Lijuan Zhang ◽  
Chen Zhang ◽  
Ming Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Meadow Soil ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Pr China ◽  
The 16S Rrna Gene

A novel Gram-stain-negative, light pink-coloured, short rod-shaped, designated strain W17T, was isolated from a meadow soil sample collected from Xinjiang, PR China. The 16S rRNA gene sequence analysis indicated that strain W17T was related most closely to Skermanella rosea M1T (98.72 %) and Skermanella mucosa 8-14-6T (98.44 %). However, strain W17T showed a low level of DNA–DNA relatedness to S. rosea M1T (32.4±2.6 %) and S. mucosa 8-14-6T (33.5±0.1 %). The genome size of the novel strain was 5.87 Mb and the genomic DNA G+C content was 67.27 mol%. The only respiratory quinone of strain W17T was Q-10. Diphosphatidylglycerol, phosphatidylglycerol. phosphatidylethanolamine and phosphatidylcholine were the major polar lipids. The predominant cellular fatty acids were C18 : 1ω6c and/or C18 : 1ω7c (48.53 %), C16 : 0 (20.88 %) and C18 : 0 (14.92 %). The phylogenetic, phenotypic and chemotaxonomic data showed that strain W17T represents a novel species of the genus Skermanella , for which the name Skermanella pratensis sp. nov. is proposed. The type strain is W17T (=GDMCC 1.1392T=KCTC 62434T).

Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yeonjae Yoo ◽  
Dongjun Kim ◽  
Hanbyul Lee ◽  
Jong Seong Khim ◽  
Bogun Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Marine Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Salt Flat ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, pale yellow-coloured, rod-shaped marine bacterium designated strain YJ-S2-02T was isolated from salt flat sediment sampled in Yongyu-do, Republic of Korea. Strain YJ-S2-02T grew at pH 6.0–9.0 (optimum, pH 7.0), 10–40 °C (optimum, 30 °C) and with optimum 1 % (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain YJ-S2-02T was closely related to Novosphingobium naphthalenivorans NBRC 102051T (97.8 %) followed by Novosphingobium mathurense SM117T (97.5 %), Novosphingobium indicum H25T (97.3 %), Novosphingobium pentaromativorans US6-1T (96.8 %), Novosphingobium fontis STM-14T (96.6 %), Novosphingobium endophyticum EGI60015T (96.5 %), Novosphingobium naphthae D39T (96.5 %) and Novosphingobium malaysiense MUSC 273T (95.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between YJ-S2-02T and related type strains were 77.0–77.9 % and 19.1–24.0 %. Strain YJ-S2-02T was characterized as having Q-10 as the predominant respiratory quinone and the principal fatty acids (>10 %) were summed feature 8 (C18 : 1  ω6c/ω7c, 20.7 %), C18 : 3  ω6c (16.3 %) and C17 : 1  ω6c (11.8 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingolipids and two unidentified lipids. The DNA G+C content of strain YJ-S2-02T was 65.6 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S2-02T should be classified as representing a novel species within the genus Novosphingobium , for which name Novosphingobium aureum is proposed, with the type strain YJ-S2-02T (=KACC 21677T =KCTC 72891T=JCM 33996T).

Algimonas ampicilliniresistens sp. nov., isolated from the red alga Porphyra yezoensis, and emended description of the genus Algimonas

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4407-4412 ◽  
Author(s):  
Youhei Fukui ◽  
Masahiro Kobayashi ◽  
Hiroaki Saito ◽  
Hiroshi Oikawa ◽  
Yutaka Yano ◽  
...  
Keyword(s):  
Type Species ◽  
Porphyra Yezoensis ◽  
Red Alga ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Emended Description

Three strains (14A-2-7T, 14A-3-1 and 14A-3) of Gram-stain-negative, prosthecate, motile bacteria were isolated from an algal medium supplemented with 10 mg ampicillin l−1 (w/v), in which the red alga Porphyra yezoensis had been cultured. Based on the 16S rRNA gene sequence analysis, the three isolates formed a cluster with the genus Algimonas of the family Hyphomonadaceae . The sequences of the three isolates had high similarity with those of Algimonas porphyrae 0C-2-2T (97.6 % similarity) and Litorimonas taeanensis G5T (95.6 % similarity). The DNA G+C contents of the three isolates ranged from 54.3 to 55.0 mol%, which were more similar to that of A. porphyrae 0C-2-2T (58.5 mol%) than to that of L. taeanensis G5T (47.1 mol%). The DNA–DNA relatedness showed that the three isolates were representatives of the same species (88.1–94.0 % relatedness) and that strain 14A-2-7T was a representative of a different species from A. porphyrae 0C-2-2T and L. taeanensis G5T (1.2–8.6 % relatedness). The phenotypic characteristics of strain 14A-2-7T differed by 20 results and 30 results from A. porphyrae 0C-2-2T and L. taeanensis G5T, respectively. The three isolates contained ubiquinone-10 as the predominant quinone and C18 : 1ω7c as the major fatty acid. Based on the polyphasic taxonomic analysis, the three isolates represent a novel species of the genus Algimonas , for which the name Algimonas ampicilliniresistens sp. nov. is proposed. The type strain is 14A-2-7T ( = LMG 26421T = NBRC 108219T). An emended description of the genus Algimonas is also proposed.

scholarly journals Algibacter marinivivus sp. nov., isolated from the surface of a marine red alga

2020 ◽  
Vol 70 (9) ◽  
pp. 5048-5053 ◽  
Author(s):  
Xian-Chun Zhong ◽  
Wei Xu ◽  
Yu Zhang ◽  
Qi-Qing Zhang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Red Alga ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Pr China ◽  
The 16S Rrna Gene

A Gram-stain-negative, non-flagellated bacterium, designated ZY111T, was isolated from the surface of a marine red alga, which was collected from the coast in Weihai, Shandong Province, PR China. Strain ZY111T exhibited growth at 4–37 °C (optimum, 25–28 °C) in the presence of 0–8.0 % (w/v) NaCl (optimum, 2.0–4.0% NaCl) and at pH 6.5–9.5 (optimum, pH 7.0–8.0). The 16S rRNA gene sequence analysis revealed that strain ZY111T belonged to the genus Algibacter , with Algibacter amylolyticus DSM 29199T as its closest relative (97.7 % similarity). The averagenucleotide identity value of strain ZY111T with A. amylolyticus DSM 29199T was 79.03 %. The digitalDNA–DNA hybridization value of strain ZY111T with A. amylolyticus DSM 29199T was 22.40 %. The dominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The sole respiratory quinone was determined to be menaquinone-6. The polar lipid profile of strain ZY111T consisted of phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. The G+C content was 31.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain ZY111T represents a novel species of the genus Algibacter , for which the name Algibacter marinivivus sp. nov. is proposed. The type strain is ZY111T (=KCTC 62373T=MCCC 1H00295T).

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