scholarly journals Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1237-1243 ◽  
Author(s):  
Diogo Neves Proença ◽  
Maria Fernanda Nobre ◽  
Paula V. Morais

Bacterial strain A37T2T was isolated from the endophytic microbial community of a Pinus pinaster tree trunk and characterized. Strain A37T2T was Gram-stain-negative, formed rod-shaped cells, and grew optimally at 26–30 °C and at pH 5.5–7.5. The G+C content of the DNA was 46.6 mol%. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were C16 : 1ω5c and iso-C15 : 0, representing 61.7 % of the total fatty acids. The polar lipids consisted of phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid, two unidentified aminolipids and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain A37T2T belonged to the family Chitinophagaceae , forming a distinct branch with Chitinophaga niabensis JS13-10T within the genus Chitinophaga . Strain A37T2T shared between 92.7 and 95.1 % 16S rRNA gene sequence similarity with the type strains of species of the genus Chitinophaga . The phylogenetic, phenotypic and chemotaxonomic data presented indicate that strain A37T2T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga costaii sp. nov. is proposed. The type strain is A37T2T ( = CIP 110584T = LMG 27458T). An emended description of Chitinophaga niabensis JS13-10T is also proposed.

2020 ◽  
Vol 70 (4) ◽  
pp. 2657-2663 ◽  
Author(s):  
Shasha Wang ◽  
Lijing Jiang ◽  
Xuewen Liu ◽  
Suping Yang ◽  
Zongze Shao

Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus Sulfurimonas , with the highest sequence similarities to Sulfurimonas crateris SN118T (97.4 %) and Sulfurimonas denitrificans DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus Sulfurimonas . On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus Sulfurimonas , for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus Sulfurimonas .


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1329-1334 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

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.


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1684-1689 ◽  
Author(s):  
Sooyeon Park ◽  
Jung-Hoon Yoon

A Gram-negative, non-spore-forming, non-flagellated, coccoid-, oval- or rod-shaped strain, designated M-M23T, was isolated from seashore sediment at Geoje island, South Korea. Strain M-M23T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain M-M23T clustered with the type strains of the two species of the genus Hirschia , with which it exhibited 97.6–98.1 % 16S rRNA gene sequence similarity. Sequence similarity with the type strains of other recognized species was <90.8 %. Strain M-M23T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain M-M23T were phosphatidylglycerol and two unidentified lipids. The DNA G+C content of strain M-M23T was 45.4 mol%. DNA–DNA relatedness between the isolate and Hirschia baltica DSM 5838T and Hirschia maritima JCM 14974T was 22±7.2 and 14±5.6 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain M-M23T is separate from the other described members of the genus Hirschia . On the basis of the data presented, strain M-M23T is considered to represent a novel species of the genus Hirschia , for which the name Hirschia litorea sp. nov. is proposed. The type strain is M-M23T ( = KCTC 32081T  = CCUG 62793T). An emended description of the genus Hirschia is also provided.


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1696-1701 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
Yong-Taek Jung

A Gram-negative, non-spore-forming, aerobic, non-flagellated, non-gliding rod, designated YCS-9T, was isolated from seawater in the South Sea, South Korea. Strain YCS-9T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain YCS-9T fell within the family Flavobacteriaceae and formed a cluster with Fulvibacter tottoriensis MTT-39T with a bootstrap resampling value of 75.4 %. Strain YCS-9T showed 92.3 % 16S rRNA gene sequence similarity to F. tottoriensis MTT-39T and 89.0–93.7 % sequence similarity to the other strains used in the phylogenetic analysis. Strain YCS-9T contained MK-6 as the only menaquinone and iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were one unidentified lipid and one unidentified aminolipid. The DNA G+C content was 34.2 mol%. Strain YCS-9T could be differentiated from F. tottoriensis NBRC 102624T by differences in fatty acid composition, polar lipid profile and some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YCS-9T represents a novel species in a new genus within the phylum Bacteroidetes , for which the name Pseudofulvibacter geojedonensis gen. nov., sp. nov. is proposed. The type strain of Pseudofulvibacter geojedonensis is YCS-9T ( = KCTC 23884T  = CCUG 62114T). An emended description of the genus Fulvibacter is also presented.


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2187-2193 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
A. Bhattacharya ◽  
P. Schumann ◽  
Syed G. Dastager ◽  
Shu-Kun Tang ◽  
...  

A Gram-positive, non-endospore-forming bacterium, designated strain SK 18T, was isolated from surface soil of a landfill site by dilution plating on trypticase soy broth agar. Preliminary characterization of strain SK 18T via biochemical tests, analysis of fatty acid methyl esters and partial 16S rRNA gene sequencing placed it within the genus Microbacterium . Analysis of the cell wall indicated that the peptidoglycan was of cross-linkage type B, containing the amino acids lysine and ornithine and with muramic acid in the N-glycolyl form. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The major fatty acids of the cell membrane were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. These data further strengthened placement of the strain within the genus Microbacterium . Strain SK 18T shared highest 16S rRNA gene sequence similarity (97.2 %) with Microbacterium ulmi DSM 16931T. Levels of similarity with the type strains of all other recognized Microbacterium species were less than 97.0 %. DNA–DNA hybridization experiments with strain SK 18T and its closest relative, M. ulmi DSM 16931T, revealed a low reassociation value of 39.0 % (σ = 3.8 %). Moreover, strain SK 18T showed a number of differences in phenotypic characteristics (colony colour, catalase activity, hydrolysis of polymers, acid production from sugars and oxidation of various substrates), and its DNA G+C content was also higher than that of M. ulmi DSM 16931T. These data indicated that strain SK 18T represents a novel species of the genus Microbacterium , for which the name Microbacterium immunditiarum sp. nov. is proposed. The type strain is SK 18T ( = MTCC 7185T = JCM 14034T). An emended description of the genus Microbacterium is also provided.


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1952-1957 ◽  
Author(s):  
Ji Hee Lee ◽  
Keun Sik Baik ◽  
Duwoon Kim ◽  
Chi Nam Seong

Two motile, rod-shaped and agarolytic bacterial strains, designated PSC101T and KDW4T, were isolated from seawater and gut microflora of abalone, respectively, collected from the South Sea (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive. Strains PSC101T and KDW4T showed high 16S rRNA gene sequence similarity to each other (98.6 %). Psychrosphaera saromensis SA4-48T was the nearest neighbour of strains PSC101T and KDW4T with 96.6 % and 97.0 % 16S rRNA gene sequence similarity, respectively. DNA–DNA relatedness among strains PSC101T, KDW4T and Psychrosphaera saromensis KCTC 23240T was less than 70 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belonged to the genus Psychrosphaera and formed a distinct phyletic line from Psychrosphaera saromensis SA4-48T. The common major cellular fatty acids of the two novel isolates were C16 : 0, C17 : 1ω8c and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). Flexirubin-type pigments were absent. The main ubiquinone was UQ-8 and the DNA G+C content of strains PSC101T and KDW4T was 49.5 and 42.5 mol%, respectively. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. On the basis of the polyphasic characterization of the two strains, it is suggested that the two isolates represent two novel species of the genus Psychrosphaera , for which the names Psychrosphaera aestuarii sp. nov. (type strain, PSC101T = KCTC 32274T = JCM 19496T) and Psychrosphaera haliotis sp. nov. (type strain, KDW4T = KCTC 22500T = JCM 16340T) are proposed. An emended description of the genus Psychrosphaera is also proposed.


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 965-970 ◽  
Author(s):  
Wen-Ming Chen ◽  
Wei-Cheng Huang ◽  
Shih-Yi Sheu

A novel nitrogen-fixing strain, designated HL-12T, was isolated from a freshwater lake in Taiwan. Cells of strain HL-12T were aerobic, Gram-negative, motile rods that were surrounded by a thick capsule, contained poly-β-hydroxybutyrate granules, and formed light-yellow to brownish-red colonies. Growth occurred at 15–40 °C (optimum 25–35 °C), at pH 6.0–7.0 (optimum pH 6.0) and with 0–4 % NaCl (optimum 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HL-12T belonged to the genus Derxia and exhibited 99.1 and 98.8 % 16S rRNA gene sequence similarity, respectively, with Derxia gummosa IAM 14990 and D. gummosa IAM 13946T. The major fatty acids (>10 %) of strain HL-12T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The cellular hydroxy fatty acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The isoprenoid quinone was Q-8 and the DNA G+C content was 72.0 mol%. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unknown aminophospholipids and phospholipids. DNA–DNA relatedness between strain HL-12T and LMG 3975 and LMG 3977T was <70 %. On the basis of the genotypic and phenotypic data, strain HL-12T represents a novel species in the genus Derxia , for which the name Derxia lacustris sp. nov. is proposed. The type strain is HL-12T ( = BCRC 80208T  = KCTC 23311T).


2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 88-94 ◽  
Author(s):  
Kornelia Kosowski ◽  
Marie Schmidt ◽  
Rüdiger Pukall ◽  
Gerd Hause ◽  
Peter Kämpfer ◽  
...  

Two strains, 8-4-E12T and 8-4-E13T, were isolated from a biowaste composting reactor. Based on 16S rRNA gene sequences, both strains belong to the genus Bacillus . Strain 8-4-E12T was most closely related to the type strains of Bacillus shackletonii , B. acidicola , B. sporothermodurans and B. oleronius (96.4, 96.3, 96.0 and 95.6 % 16S rRNA gene similarity, respectively), whereas strain 8-4-E13T was most closely related to the type strain of Bacillus humi (96.5 % sequence similarity). Strains 8-4-E12T and 8-4-E13T shared 94 % 16S rRNA gene sequence similarity. The fatty acid profile of strain 8-4-E12T was dominated by saturated iso- and anteiso-branched fatty acids (iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0), and also contained considerable amounts of C16 : 0. The fatty acid profile of strain 8-4-E13T showed a predominance of iso-C15 : 0 (65 %), with smaller amounts of other saturated branched-chain fatty acids along with an unsaturated alcohol. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids. Additionally, strain 8-4-E12T contained an unknown lipid and strain 8-4-E13T two unknown (amino-)phospholipids. The diagnostic diamino acid found in the cell-wall peptidoglycan of 8-4-E12T and 8-4-E13T was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The results of physiological and biochemical tests also allowed phenotypic differentiation of the two strains from each other and from related Bacillus species. On the basis of their phylogenetic, phenotypic and chemotaxonomic properties, strains 8-4-E12T and 8-4-E13T represent novel species of the genus Bacillus , for which the names Bacillus pervagus sp. nov. (type strain 8-4-E12T = DSM 23947T = LMG 27601T) and Bacillus andreesenii sp. nov. (type strain 8-4-E13T = DSM 23948T = LMG 27602T) are proposed.


2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2223-2228 ◽  
Author(s):  
Gabriel Paiva ◽  
Pedro Abreu ◽  
Diogo Neves Proença ◽  
Susana Santos ◽  
Maria Fernanda Nobre ◽  
...  

Bacterial strain M47C3BT was isolated from the endophytic microbial community of a Pinus pinaster tree branch from a mixed grove of pines. Phylogenetic analysis of 16S rRNA gene sequences showed that this organism represented one distinct branch within the family Sphingobacteriaceae , most closely related to the genus Mucilaginibacter . Strain M47C3BT formed a distinct lineage, closely related to Mucilaginibacter dorajii KACC 14556T, with which it shared 97.2 % 16S rRNA gene sequence similarity. The other members of the genus Mucilaginibacter included in the same clade were Mucilaginibacter lappiensis ATCC BAA-1855T sharing 97.0 % similarity and Mucilaginibacter composti TR6-03T that had a lower similarity (95.7 %). The novel strain was Gram-staining-negative, formed rod-shaped cells, grew optimally at 26 °C and at pH 7, and was able to grow with up to 0.3 % (w/v) NaCl. The respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids of the strain were summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH, representing 73.5 % of the total fatty acids. The major components of the polar lipid profile of strain M47C3BT consisted of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The G+C content of the DNA was 40.6 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics we propose the name Mucilaginibacter pineti sp. nov. for the novel species represented by strain M47C3BT ( = CIP 110632T = LMG 28160T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 777-782 ◽  
Author(s):  
Stefanie P. Glaeser ◽  
Enevold Falsen ◽  
Hans-Jürgen Busse ◽  
Peter Kämpfer

A Gram-positive-staining, aerobic, endospore-forming bacterium, isolated from a necrotic wound of a 35-year-old man was studied in detail to determine its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain CCUG 53270T was grouped into the genus Paenibacillus , most closely related to the type strains of Paenibacillus rigui (97.2 %), Paenibacillus xylanisolvens (96.3 %) and Paenibacillus chinjuensis (96.1 %). The 16S rRNA gene sequence similarity to strains of other Paenibacillus species was ≤96 %. Chemotaxonomic characterization supported the allocation of the strain to the genus Paenibacillus . The major menaquinones were MK-7 (85 %) and MK-6 (15 %). The polar lipid profile contained the major compounds diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The polyamine pattern contained predominantly spermidine. The major fatty acids were iso- and anteiso-branched fatty acids. The results of physiological and biochemical tests allowed phenotypic differentiation of strain CCUG 53270T from closely related species. Thus, strain CCUG 53270T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus vulneris sp. nov. is proposed, with CCUG 53270T ( = JCM 18268T) as the type strain.


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