scholarly journals Streptomyces lycii sp. nov., an endogenous actinomycete isolated from Lycium ruthenicum

2020 ◽  
Vol 70 (10) ◽  
pp. 5197-5204 ◽  
Author(s):  
Liran Ma ◽  
Hong Zeng ◽  
Zhanfeng Xia ◽  
Xiaoxia Luo ◽  
Lili Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Lycium Ruthenicum

A novel endogenous actinobacteria strain, designated TRM 66187T, was isolated from Lycium ruthenicum sampled at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66187T with the genus Streptomyces . The whole-cell sugar pattern of TRM 66187T consisted of galactose, glucose and ribose. The predominant menaquinones were MK-9(H4) and MK-9(H6). Major cellular fatty acids were iso-C14:0, iso-C15:0, anteiso-C15:0 and anteiso-C16:0. The detected polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified polar lipids. The G+C content of strain TRM 66187T was 71.8 mol%. Results of phylogenetic analysis showed that strain TRM 66187T had 98.48% 16S rRNA gene sequence similarity to the closest described species Streptomyces qinglanensis DSM 42035T. The average nucleotide identity value between strain TRM 66187T and the closest related strain Streptomyces qinglanensis DSM 42035T was calculated to be 77.2%. The digital DNA–DNA hybridization value between them was 22.4%. Multilocus sequence analyses based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also indicated that strain TRM 66187T should be assigned to the genus Streptomyces . On the basis of evidence from this polyphasic study, strain TRM 66187T should be designated as representing a novel species of the genus Streptomyces , for which the name Streptomyces lycii sp. nov. is proposed. The type strain is TRM 66187T (=LMG 31493T=CCTCC AA 2018094T).

Mariniflexile jejuense sp. nov., isolated from the junction between seawater and a freshwater spring, and emended description of the genus Mariniflexile

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1329-1334 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Freshwater Spring

A Gram-negative, non-spore-forming, non-flagellated, motile-by-gliding rod, designated SSK2-3T, was isolated from the junction between seawater and a freshwater spring at Jeju island, South Korea. Strain SSK2-3T grew optimally at 25–30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SSK2-3T clustered with type strains of species of the genus Mariniflexile , with which it exhibited 97.2–97.8 % 16S rRNA gene sequence similarity. Sequence similarity between the isolate and the other strains used in the phylogenetic analysis was <95.6 %. Strain SSK2-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G and C15 : 0 as the major fatty acids. The major polar lipids of strain SSK2-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-3T was 32.4 mol%. DNA–DNA relatedness between the isolate and Mariniflexile gromovii KCTC 12570T, Mariniflexile fucanivorans DSM 18792T and Mariniflexile aquimaris HWR-17T was 19, 15 and 20 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK2-3T is separate from other members of the genus Mariniflexile . On the basis of the data presented, strain SSK2-3T is considered to represent a novel species of the genus Mariniflexile , for which the name Mariniflexile jejuense sp. nov. is proposed. The type strain is SSK2-3T ( = KCTC 23958T  = CCUG 62414T). An emended description of the genus Mariniflexile is given.

Psychroflexus halocasei sp. nov., isolated from a microbial consortium on a cheese

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1850-1856 ◽  
Author(s):  
Herbert Seiler ◽  
Anne Bleicher ◽  
Hans-Jürgen Busse ◽  
Josef Hüfner ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A novel halophilic, Gram-reaction-negative, strictly aerobic, non-motile, rod-shaped and oxidase- and catalase-positive bacterial strain, designated WCC 4520T, was isolated from a semi-hard, Raclette-type cheese. The colonies were yellow–orange; flexirubin-type pigments were not found. The strain hydrolysed gelatin, hippurate, tyrosine and Tweens 20 and 80. Optimal growth was observed with 6–8 % (w/v) NaCl, at pH 7–8 and at 27–30 °C. The genomic DNA G+C content was 33.6 mol%. In phylogenetic analysis based on 16S rRNA gene sequences, strain WCC 4520T appeared to be a member of the family Flavobacteriaceae and the closest phylogenetic neighbours were identified as Psychroflexus gondwanensis DSM 5423T (94.0 % 16S rRNA gene sequence similarity) and Psychroflexus salinarum CCUG 56752T (94.0 %). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The only detected quinone was MK-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified polar lipid. Minor polar lipids and traces of polyamines were also detected. On the basis of the data presented, strain WCC 4520T represents a novel species of the genus Psychroflexus , for which the name Psychroflexus halocasei sp. nov. is proposed. The type strain is WCC 4520T ( = LMG 25857T = CCUG 59705T).

scholarly journals Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3215-3221 ◽  
Author(s):  
Manziram Rozahon ◽  
Nurimangul Ismayil ◽  
Buayshem Hamood ◽  
Raziya Erkin ◽  
Mehfuzem Abdurahman ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Populus Euphratica ◽  
Endophytic Bacterium ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

An endophytic bacterium, designated K-38T, was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38T was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38T grew at temperatures of 25–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0–3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38T was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3T, followed by Rhizobium nepotum 39/7T (96.5 %) and Rhizobium borbori DN316T (96.2 %). Phylogenetic analysis of strain K-38T based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium . The DNA G+C content was determined to be 63.5 mol%. DNA–DNA relatedness between K-38T and R. rosettiformans W3T was 48.4 %, indicating genetic separation of strain K-38T from the latter strain. The major components of the cellular fatty acids in strain K-38T were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38T include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38T. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38T represents a novel species of the genus Rhizobium , for which the name Rhizobium populi sp. nov. is proposed. The type strain is K-38T ( = CCTCC AB 2013068T = NRRL B-59990T = JCM 19159T).

scholarly journals Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis)

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1561-1566 ◽  
Author(s):  
Jin-Hua Chen ◽  
Xiang-Rong Tian ◽  
Ying Ruan ◽  
Ling-Ling Yang ◽  
Ze-Qiang He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Crassostrea Hongkongensis ◽  
Link Type

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 °C (optimum 30–35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118T belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211T (98.9 % 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33T (98.3 %), Bacillus niabensis 4T19T (97.8 %) and Bacillus herbersteinensis D-1,5aT (97.1 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118T represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118T ( = CCTCC AB 2010452T = DSM 24486T = JCM 17523T).

scholarly journals Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4115-4119 ◽  
Author(s):  
Parisa Zarparvar ◽  
Mohammad Ali Amoozegar ◽  
Mahdi Moshtaghi Nikou ◽  
Peter Schumann ◽  
Antonio Ventosa
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A halophilic actinomycete, strain R4S8T, was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30–50 °C (optimum 40 °C), pH 6–10 (optimum pH 7.0) and in the presence of 1–15 % (w/v) NaCl (optimum 3–5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8T contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8T belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269T (95.5 %) and Marininema mesophilum SCSIO 10219T (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8T represents a novel species in a new genus within the family Thermoactinomycetaceae , for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8T ( = IBRC-M 10813T = CECT 8506T).

scholarly journals Psychroglaciecola arctica gen. nov., sp. nov., isolated from Arctic glacial foreland soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1817-1824 ◽  
Author(s):  
Zhihao Qu ◽  
Fan Jiang ◽  
Xulu Chang ◽  
Xia Qiu ◽  
Lvzhi Ren ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Svalbard Archipelago ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel pink-pigmented, facultatively methylotrophic strain, designated M6-76T, was isolated from glacial foreland soil near Ny-Ålesund, Svalbard Archipelago, Norway. Cells of strain M6-76T were rod-shaped (0.4–0.7×0.8–2.0 µm), Gram-stain-negative, aerobic and motile by a single polar flagellum. Growth occurred at 4–28 °C (optimum 18 °C) and at pH 5–8 (optimum pH 7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M6-76T belonged to the family Methylobacteriaceae . The 16S rRNA gene sequence of the novel strain showed 94.6 %, 94.0 % and 93.9 % sequence similarity to those of Methylobacterium salsuginis MRT, Methylobacterium organophilum ATCC 27886T and Microvirga subterranea FaiI4T, respectively. Cells could utilize methanol as the sole source of carbon and energy but not formate. The major respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown polar lipids. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0. The DNA G+C content was 67 mol%. The polyphasic data presented in this study indicated that the isolate should be classified as representing a novel species of a new genus within the family Methylobacteriaceae . The name Psychroglaciecola arctica gen. nov., sp. nov. is therefore proposed for the isolate. The type strain of the type species is M6-76T ( = CCTCC AB 2013033T = KACC 17684T).

Pedobacter riviphilus sp. nov., isolated from stream sediment

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Hong Sik Im ◽  
Yochan Joung ◽  
Sang-Seob Lee
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Small Stream ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae . Phylogenetic analysis also showed that strain SW-16T was most closely related to Pedobacter soli 15-51T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135T (97.5%), Pedobacter suwonensis 15-52T (97.4%), Pedobacter sandarakinus DS-27T (97.0%) and Pedobacter kyungheensis THG-T17T (97.0%). Growth was observed at 10–37 °C (optimum at 30 °C), pH 6–8 (optimum at pH 7) and with 0–2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16T represents a novel species of the genus Pedobacter , for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16T (=KEMB 1602–396T=KCTC 82079T=JCM 34181T).

Ferruginibacter yonginensis sp. nov., isolated from a mesotrophic artificial lake

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 846-850 ◽  
Author(s):  
Beom-Il Lee ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Yochan Joung ◽  
Kiseong Joh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Artificial Lake ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, rod-shaped, aerobic and reddish-pigmented strain, designated HME8442T, was isolated from a mesotrophic artificial lake. The strain grew optimally at 30 °C and pH 7 on R2A agar. The major fatty acid was iso-C15 : 0. The polar lipids were phosphatidylethanolamine, one unidentified aminolipid and three unidentified polar lipids. The predominant respiratory quinone was MK-7. The DNA G+C content was 35.8 mol%. Strain HME8442T was closely related to Ferruginibacter lapsinanis HU1-HG42T (94.4 % 16S rRNA gene sequence similarity) and Ferruginibacter alkalilentus HU1-GD23T (93.9 %). The phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8442T formed a lineage within the genus Ferruginibacter . On the basis of the evidence presented in this study, strain HME8442T represents a novel species of the genus Ferruginibacter , for which the name Ferruginibacter yonginensis sp. nov. is proposed. The type strain is HME8442T ( = KACC 17314T = CECT 8289T).

Pseudahrensia aquimaris gen. nov., sp. nov., isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2056-2061 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated HDW-32T, was isolated from seawater of the Yellow Sea, Korea. Strain HDW-32T grew optimally at pH 7–8, at 30 °C and with 2–3 % (w/v) NaCl. Strain HDW-32T exhibited 95.1 % 16S rRNA gene sequence similarity with Nitratireductor basaltis J3T, 94.8 % sequence similarity with Ahrensia kielensis IAM 12618T and <94.5 % with other members of the family Phyllobacteriaceae . In the neighbour-joining, maximum-likelihood and maximum-parsimony trees based on 16S rRNA gene sequences, strain HDW-32T clustered with A. kielensis IAM 12618T. Strain HDW-32T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. Differences in polar lipids, DNA G+C content and other phenotypic properties distinguished strain HDW-32T from A. kielensis JCM 20689T. Strain HDW-32T could also be distinguished from representatives of the genera Nitratireductor and Hoeflea by differences in fatty acids and polar lipids. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain HDW-32T represents a novel species belonging to a novel genus of the family Phyllobacteriaceae of the class Alphaproteobacteria , for which the name Pseudahrensia aquimaris gen. nov., sp. nov. is proposed. The type strain of the type species is HDW-32T ( = KCTC 23345T  = CCUG 60023T).

Advenella faeciporci sp. nov., a nitrite-denitrifying bacterium isolated from nitrifying–denitrifying activated sludge collected from a laboratory-scale bioreactor treating piggery wastewater

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2986-2990 ◽  
Author(s):  
Masaki Matsuoka ◽  
Sanghwa Park ◽  
Sun-Young An ◽  
Morio Miyahara ◽  
Sang-Wan Kim ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Piggery Wastewater ◽  
Content Type ◽  
Link Type

Strain M-07T was isolated from nitrifying–denitrifying activated sludge treating piggery wastewater. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain M-07T belonged to the genus Advenella . 16S rRNA gene sequence similarity between M-07T and Advenella incenata CCUG 45225T, Advenella mimigardefordensis DPN7T and Advenella kashmirensis WT001T was 96.5, 97.3 and 96.9 %, respectively. The DNA G+C content of strain M-07T was 49.5 mol%, which was approximately 5 mol% lower than the range for the genus Advenella (53.5–58.0 mol%). The predominant cellular fatty acids of strain M-07T were C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 0 cyclo and summed feature 2 (comprising one or more of C14 : 0 3-OH, iso-C16 : 1 I, an unidentified fatty acid with an equivalent chain-length of 10.928 and C12 : 0 alde). The isoprenoid quinone was Q-8. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, strain M-07T should be classified as a novel species of the genus Advenella , for which the name Advenella faeciporci sp. nov. is proposed. The type strain is M-07T ( = JCM 17746T  = KCTC 23732T).

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