Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 1972-1981 ◽  
Author(s):  
Taishi Tsubouchi ◽  
Yasuhiro Shimane ◽  
Kozue Mori ◽  
Keiko Usui ◽  
Toshiki Hiraki ◽  
...  

A novel filamentous bacterium, designated strain JIR-001T, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family Thermoactinomycetaceae . Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001T belongs to the family Thermoactinomycetaceae within the class Bacilli . Similarity levels between the 16S rRNA gene sequence of strain JIR-001T and those of the type strains of Thermoactinomycetaceae species were 85.5–93.5 %; highest sequence similarity was with Melghirimyces algeriensis NariEXT. In the DNA–DNA hybridization assays between strain JIR-001T and its phylogenetic neighbours the mean hybridization levels with Melghirimyces algeriensis NariEXT, Planifilum fimeticola H0165T, Planifilum fulgidum 500275T and Planifilum yunnanense LA5T were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001T was 55.1 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001T is considered to represent a novel species in a new genus of the family Thermoactinomycetaceae , for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001T ( = JCM 18147T = CECT 8074T).

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).


2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1419-1427 ◽  
Author(s):  
Peter Kämpfer ◽  
Marie T. Poppel ◽  
Gottfried Wilharm ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
...  

Two yellow-pigmented bacterial strains (100T and C26T), showing 98.4 % 16S rRNA gene sequence similarity to each other and isolated from a chicken in Germany and as a contaminant from an agar plate of a rhizosphere sample in Alabama, were studied by using a polyphasic taxonomic approach. Cells of both isolates were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequences of the two organisms with the sequences of the type strains of the most closely related species of the genus Chryseobacterium showed the highest sequence similarities of strains 100T and C26T to the type strains of Chryseobacterium joostei (respectively 97.5 and 98.2 %), C. viscerum (96.6, 97.8 %), C. gleum (97.1, 97.7 %), C. arthrosphaerae (97.3%, 97.7 %), C. indologenes (97.2, 97.7 %), C. tructae (96.6, 97.6 %), C. jejuense (97.0, 97.6 %) and C. oncorhynchi (96.3, 97.5 %); 16S rRNA gene sequence similarities to members of all other species of the genus Chryseobacterium were below 97.5 %. The fatty acid profiles of both strains consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH, but also showed slight differences (absence or presence of C16 : 0 3-OH and iso-C15 : 1 F). DNA–DNA hybridizations between the two strains and between the novel strains and the type strains of C. joostei , C. indologenes , C. jejuense , C. tructae and C. viscerum resulted in relatedness values clearly below 70 %. These DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed that both strains 100T and C26T represent novel species, for which the names Chryseobacterium gallinarum sp. nov. (type strain 100T = LMG 27808T = CCM 8493T) and Chryseobacterium contaminans sp. nov. (type strain C26T = LMG 27810T = CCM 8492T) are proposed.


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1403-1410 ◽  
Author(s):  
Yun-Hee Jang ◽  
Soo-Jin Kim ◽  
Tomohiko Tamura ◽  
Moriyuki Hamada ◽  
Hang-Yeon Weon ◽  
...  

A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Microbacteriaceae . The nearest phylogenetic neighbour was Leifsonia kribbensis MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and Leifsonia kribbensis MSL-13T formed a distinct cluster within the family Microbacteriaceae . Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1876-1881 ◽  
Author(s):  
Sooyeon Park ◽  
Sung-Min Won ◽  
Doo-Sang Park ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, AH-M5T, which was isolated from a tidal flat sediment at Aphae Island in South Korea, was characterized taxonomically. Strain AH-M5T grew optimally at 25 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain AH-M5T clustered coherently with the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus , showing 93.4–94.3 % sequence similarity. The novel strain exhibited 16S rRNA gene sequence similarity values of less than 93.4 % to the type strains of other recognized species. Strain AH-M5T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The polar lipid profile of strain AH-M5T containing phosphatidylethanolamine and one unidentified lipid as major components was differentiated from those of the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . The DNA G+C content of strain AH-M5T was 34.8 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain AH-M5T is distinguished from Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . On the basis of the data presented, strain AH-M5T is considered to represent a novel genus and species within the family Flavobacteriaceae , for which the name Seonamhaeicola aphaedonensis gen. nov., sp. nov. is proposed. The type strain of the type species is AH-M5T ( = KCTC 32578T = CECT 8487T).


2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4552-4556 ◽  
Author(s):  
Jie Li ◽  
Sheng Qin ◽  
Zhi-Qing You ◽  
Li-Juan Long ◽  
Xin-Peng Tian ◽  
...  

A novel filamentous bacterium, strain SCSIO 11153T, was isolated from a sediment sample collected from the Indian Ocean (80° 03.099′ E 01° 03.300′ N) at a depth of 4593 m. Good growth was observed at 50–55 °C and pH 7.0 with 3 % NaCl. It formed ivory–white colonies with radial wrinkles. Aerial mycelium was absent on the media tested. Phenotypic characteristics and 16S rRNA gene sequence analysis indicated that strain SCSIO 11153T belonged to the family Thermoactinomycetaceae . It exhibited 96.4 % and 96.2 % 16S rRNA gene sequence similarities to Melghirimyces algeriensis NariEXT and Melghirimyces thermohalophilus Nari11AT, respectively, while lower sequence similarity values (<95.4 %) were observed between strain SCSIO 11153T and other species of genera in the family Thermoactinomycetaceae . The menaquinone type was MK-7. Major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain SCSIO 11153T was 52.6 mol%. On the basis of the genotypic and phenotypic characteristics, it is proposed that strain SCSIO 11153T represents a novel species of the genus Melghirimyces with the name Melghirimyces profundicolus sp. nov. The type strain is SCSIO 11153T ( = DSM 45787T = CCTCC AA 2012007T = NBRC 109068T).


2020 ◽  
Vol 70 (11) ◽  
pp. 5824-5831 ◽  
Author(s):  
Peter Kämpfer ◽  
S. P. Glaeser ◽  
John A. McInroy ◽  
Jia Xu ◽  
Hans-Jürgen Busse ◽  
...  

A Gram-staining-negative non endospore-forming strain, PXU-55T, was isolated from the rhizosphere of the switchgrass Panicum virgatum and studied in detail to determine its taxonomic position. The results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Flavobacterium . The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.78 %) and Flavobacterium chilense (98.64 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the PXU-55T genome assembly and the ones of the most closely related type strains of species of the genus Flavobacterium were 87.3 and 31.9% ( Flavobacterium defluvii ), and 86.1 and 29.9% ( Flavobacterium johnsoniae ). Menaquinone MK-6 was the major respiratory quinone. As major polar lipids, phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L2, L3 and L4 lacking a functional group were found. Moderate to minor amounts of another ornithine lipid, the unidentified lipid L1 and a glycolipid were present, as well. The major polyamine is sym-homospermidine. The fatty acid profiles contained major amounts of iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso C16:0 3-OH, C16:0 3-OH and C15:0 3-OH, which supported the classification of the isolate as a member of the genus Flavobacterium . Physiological and biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. For this reason, we propose that strain PXU-55T (=CIP 111646T=CCM 8914T) represents a novel species with the name Flavobacterium panici sp. nov.


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 945-951 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod- or coccoid-shaped bacterial strain, designated HD-22T, 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 HD-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HD-22T fell within the clade comprising species of the genus Jannaschia , clustering with the type strains of Jannaschia helgolandensis , Jannaschia donghaensis and Jannaschia rubra , with which it exhibited highest 16S rRNA gene sequence similarity (97.6–98.2 %). Levels of 16S rRNA gene sequence similarity between strain HD-22T and the type strains of the other species of the genus Jannaschia were in the range 94.4–97.5 %. The DNA G+C content was 64.6 mol% and mean DNA–DNA relatedness values between strain HD-22T and the type strains of J. helgolandensis , J. donghaensis and J. rubra were 42.1, 40.1 and 27.0 %, respectively. Strain HD-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain HD-22T is distinguishable from recognized species of the genus Jannaschia . On the basis of the data presented, strain HD-22T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia faecimaris sp. nov. is proposed. The type strain is HD-22T ( = KCTC 32179T = CCUG 63415T).


2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4118-4123 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated D1-W3T, was isolated from tidal flat sediment of the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain D1-W3T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic analyses based on 16S rRNA gene sequences revealed that strain D1-W3T fell within the clade comprising species of the genus Loktanella , clustering with the type strains of Loktanella tamlensis , Loktanella rosea and Loktanella maricola , with which it exhibited the highest 16S rRNA gene sequence similarity values (98.1–98.2 %). The 16S rRNA gene sequence similarity values between strain D1-W3T and the type strains of other species of the genus Loktanella were in the range 93.5–96.5 %. The DNA G+C content of strain D1-W3T was 58.1 mol% and the mean DNA–DNA hybridization values with L. tamlensis KCTC 12722T, L. rosea LMG 22534T and L. maricola DSW-18T were 13–25 %. Strain D1-W3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain D1-W3T could be differentiated from other species of the genus Loktanella . On the basis of the data presented, strain D1-W3T represents a novel species of the genus Loktanella , for which the name Loktanella sediminilitoris sp. nov. is proposed. The type strain is D1-W3T ( = KCTC 32383T = CECT 8284T).


2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2383-2387 ◽  
Author(s):  
Huili Pang ◽  
Maki Kitahara ◽  
Zhongfang Tan ◽  
Yanping Wang ◽  
Guangyong Qin ◽  
...  

Characterization and identification of strain CW 1 ( = JCM 17161) isolated from corn silage were performed. Strain CW 1 was a Gram-positive, catalase-negative and homofermentative rod that produced the dl-form of lactic acid. This strain exhibited more than 99.6 % 16S rRNA gene sequence similarity and greater than 82 % DNA–DNA reassociation with type strains of Lactobacillus kimchii , L. bobalius and L. paralimentarius . To clarify the taxonomic positions of these type strains, phenotypic characterization, 16S rRNA gene sequencing, ribotyping and DNA–DNA relatedness were examined. The three type strains displayed different l-arabinose, lactose, melibiose, melezitose, raffinose and N-acetyl-β-glucosaminidase fermentation patterns. Phylogenetic analysis showed that L. paralimentarius is a closer neighbour of L. kimchii and L. bobalius , sharing 99.5–99.9 % 16S rRNA gene sequence similarity, which was confirmed by the high DNA–DNA relatedness (≥82 %) between L. paralimentarius JCM 10415T, L. bobalius JCM 16180T and L. kimchii JCM 10707T. Therefore, it is proposed that L. kimchii and L. bobalius should be reclassified as later synonyms of L. paralimentarius .


Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
Stefanie P. Glaeser ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  

A Gram-stain-positive, non-motile, non-spore-forming, coccus (strain Do 184T) was isolated from exhaust air of a turkey fattening plant on mannitol salt agar. The strain shared high 16S rRNA gene sequence similarity to the type strains of Jeotgalicoccus aerolatus (98.0%) followed by Jeotgalicoccus marinus (97.2%) and Jeotgalicoccus huakuii (97.1%). All other 16S rRNA gene sequence similarities to species of the genus Jeotgalicoccus were below 97%. The average nucleotide identities (ANI) between the Do 184T genome assembly and the ones of type strains of species of the genus Jeotgalicoccus were far below the 95% species delineation cutoff value, ranging from 79.47% ( J. marinus DSM 19772T) to 75.30% ( J. pinnipedialis CIP 107946T). The quinone system of Do 184T, the polar lipid profile, the polyamine pattern and the fatty acid profile were in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of Do 184T to this genus. Do 184T represents a novel species, for which the name Jeotgalicoccus meleagridis sp. nov. is proposed, with the type strain Do 184T (=LMG 31100T=CCM 8918T=CIP 111649T). In addition, data on genome sequences of Jeotgalicoccus halophilus C1-52T =CGMCC 1.8911T=NBRC 105788T and Jeotgalicoccus aerolatus MPA-33T=CCM 7679T=CCUG 57953T=DSM 22420T=CIP 111750T indicate that both isolates represent the same species. Pairwise ANI between the genomes of these two strains lead to similarities of 98.98–99.05 %. These results indicate that these strains represent members of the same species. Due to priority of publication it is proposed that Jeotgalicoccus halophilus is reclassified as Jeotgalicoccus aerolatus .


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