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    A study of three bacteria isolated from marine sediment and description of Micromonospora globispora sp. nov.
    (Elsevier Gmbh, 2019) Carro, Lorena; Veyisoglu, Aysel; Cetin, Demet; Igual, Jose M.; Klenk, Hans-Peter; Trujillo, Martha E.; Sahin, Nevzat
    During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901(T), S2903, and S2904. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, meso-diaminopimelic acid in the wall peptidoglycan, a tetrahydrogenated menaquinone with nine isoprene units as major respiratory quinone, iso-C-15:0 and iso-C-16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strain S2901(T), S2903, and S2904 showed the highest similarity (99.2%) with the type strain of Micromonospora halophytica DSM 43171(T), forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with gyrB gene and MLSA phylogenies. Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the isolates should be assigned to a new species within the genus Micromonospora for which the name Micromonospora globispora sp. nov. (S2901(T), S2903 and S2904) is proposed. (C) 2018 Elsevier GmbH. All rights reserved.
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    Genomic Analysis of a Novel Heavy Metal Resistant Isolate from a Black Sea Contaminated Sediment with the Potential to Degrade Alkanes: Plantactinospora alkalitolerans sp. nov.
    (Mdpi, 2022) Carro, Lorena; Veyisoglu, Aysel; Guven, Kiymet; Schumann, Peter; Klenk, Hans-Peter; Sahin, Nevzat
    Microorganisms that grow in poorly studied environments are of special interest when new biotechnological applications are searched. The Melet river offshore sediments at the Black Sea have been described to contain an important number of contaminants from upstream industries which have been accumulating for years. Bacteria of such habitats must be adapted to the presence of those compounds and in some cases, are able to use them as carbon sources. In the analysis of some samples recovered from this environment, an actinobacterial strain was isolated, named as S1510(T), and its taxonomic position was determined using a combination of phenotypic and genotypic properties. Strain S1510(T) presented phenotypic properties typical of members of the family Micromonosporaceae and was assigned to the Plantactinospora genus, based on the phylogenetic analyses of the 16S rRNA gene and whole-genome sequences. Low dDDH (digital DNA-DNA hybridization) values with other members of the genus confirmed that Plantactinospora sp. S1510(T) represents a novel species, and is proposed with the new name Plantactinospora alkalitolerans. The strain presented characteristics not previously described for other species in the genus, such as its high tolerance to alkaline pHs, the presence of genes related to the production and degradation of alkanes (oleABCD, ssuAD, almA), the degradation of several aromatic compounds, and the tolerance to high heavy metal concentrations. In addition, Plantactinospora sp. S1510(T) presents several bioclusters to produce nonribosomal peptide-synthetases, terpenes, polyketide synthases, and bacteriocins, that possess low similarities with known compounds.
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    Micromonospora orduensis sp. nov., isolated from deep marine sediment
    (Springer, 2020) Veyisoglu, Aysel; Carro, Lorena; Cetin, Demet; Igual, Jose M.; Klenk, Hans-Peter; Sahin, Nevzat
    A novel actinobacterial strain, designated S2509(T), was isolated from marine sediment collected by a dredge at a depth of 45 m along Melet River offshore of the southern Black Sea coast, Ordu, Turkey. The cell wall peptidoglycan of strain was found to contain meso-diaminopimelic acid and 3-OH-diaminopimelic acid. The whole cell sugars detected were arabinose, glucose, rhamnose, ribose and xylose. The diagnostic phospholipids of strain S2509(T) were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The predominant menaquinones were identified as MK-9(H-8), MK-9(H-6), MK-10(H-8), MK-9(H-4), MK-10(H-4) and MK-10(H-6). The major cellular fatty acids were found to be iso-C-16:0, iso-C-15:0 and 10-methyl C-17:0. The taxonomic position of the strain was established using a polyphasic approach, showing that S2509(T) strain belongs to the genus Micromonospora. Phylogenetic analysis based on the 16S rRNA gene sequence of strain S2509(T) showed that it is closely related to the type strain of Micromonospora chokoriensis DSM 45160(T) (99.37% sequence similarity), and phylogenetically clustered with Micromonospora inaquosa LB39(T) (99.37%), Micromonospora lupini Lupac 14N(T) (99.16%), Micromonospora violae NEAU-zh8(T) (99.23%) and Micromonospora taraxaci NEAU-P5(T) (99.03%). The phylogenetic analysis based on the gyrB gene sequence of strain S2509(T) confirmed its close relationship with M. chokoriensis JCM 13247(T) (96.5% sequence similarity). Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the strain S2509(T) represents a novel species in the genus Micromonospora, for which the name Micromonospora orduensis sp. nov. is proposed. The type strain is S2509(T) (=DSM 45926(T) = KCTC 29201(T)).
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    Micromonospora phytophila sp nov and Micromonospora luteiviridis sp nov., isolated as natural inhabitants of plant nodules
    (Microbiology Soc, 2018) Carro, Lorena; Veyisoglu, Aysel; Riesco, Raul; Sproeer, Cathrin; Klenk, Hans-Peter; Sahin, Nevzat; Trujillo, Martha E.
    Two actinobacterial isolates, strains SG15(T) and SGB14(T), were recovered through a microbial diversity study of nitrogen fixing nodules from Pisum sativum plants collected in Salamanca (Spain). The taxonomic status of these isolates was determined using a polyphasic approach and both presented chemotaxonomic and morphological properties consistent with their classification in the genus Micromonospora. For strains SG15(T) and SGB14(T), the highest 16S rRNA gene sequence similarities were observed with Micromonospora coxensis JCM 13248(T) (99.2 %) and Micromonospora purpureochromogenes DSM 43821(T) (99.4 %), respectively. However, strains SG15(T) and SGB14(T) were readily distinguished from their phylogenetic neighbours both genetically and phenotypically indicating that they represent two new Micromonospora species. The following names are proposed for these species: Micromonospora phytophila sp. nov. type strain SG15(T) (=CECT 9369(T); =DSM 105363(T)), and Micromonospora luteiviridis sp. nov. type strain SGB14(T) (=CECT 9370(T); =DSM 105362(T)).
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    Phytomonospora cypria sp nov., isolated from soil
    (Springer, 2015) Sahin, Nevzat; Veyisoglu, Aysel; Tatar, Demet; Saygin, Hayrettin; Cetin, Demet; Guven, Kiymet; Klenk, Hans-Peter
    A Gram-stain positive actinobacterial strain, designated KT1403(T), was isolated from a soil sample, collected from Karpaz, Magusa, Northern Cyprus, and characterised using a polyphasic approach. Morphological characteristics and chemotaxonomic data indicated that the strain belongs to the genus Phytomonospora. The cell wall of the novel strain contained meso-diaminopimelic acid and galactose, glucose and mannose as the major sugars in whole cell hydrolysates. The polar lipids in the cell membrane were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified aminophospholipid and three unidentified glycolipids. The predominant menaquinones were MK-10(H-6) and MK-10(H-4). The major fatty acids were found to be iso C-15:0 , anteiso C-15:0 and anteiso C-17:0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KT1403(T) belongs to the genus Phytomonospora with a sequence similarity of 99.73 % with Phytomonospora endophytica, the type species of the genus. DNA-DNA hybridization further differentiated strain KT1403(T) from its near phylogenetic neighbour, P. endophytica DSM 45386(T) (29.0 +/- A 2.2 % DNA relatedness). Therefore, it is proposed that strain KT1403(T) represents a novel species of the genus Phytomonospora, for which the name Phytomonospora cypria sp. nov. is proposed. The type strain is KT1403(T) (=KCTC 29479(T) = DSM 46767(T)).
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    Saccharopolyspora hattusasensis sp nov., isolated from soil
    (Springer, 2017) Veyisoglu, Aysel; Saygin, Hayrettin; Tatar, Demet; Bektas, Kadriye Inan; Sahin, Nevzat
    A Saccharopolyspora strain, designated CR3506(T), isolated from a soil sample collected from Sungurlu, Corum, Turkey, was examinated using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence analysis showed that the strain is closely related to the type strains of Saccharopolyspora spinosa NRRL 18395(T) (99.1%), Saccharopolyspora phatthalungensis NRRL B-24798(T) (98.4%) and Saccharopolyspora shandongensis 88(T) (98.1%); low levels of DNA-DNA relatedness were found between the isolate and S. spinosa and S. phatthalungensis (< 50%). Strain CR3506(T) was found to have chemotaxonomic and phylogenetic properties consistent with its classification in the genus Saccharopolyspora. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The polar lipids were identified as phosphatidylmethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones (> 10%) were MK-9(H-4) and MK-8(H-4). Major fatty acids were (> 10%) iso-C-16:0, C(15:0)3OH, C-18:0 and iso-C-15:0. Further, the morphological, physiological and biochemical characteristics of strain CR3506(T) are distinct from S. spinosa and other species of the genus Saccharopolyspora with which this strain has high 16S rRNA gene sequence similarity (98.0-98.5%). Strain CR3506(T) has antimicrobial activity against Bacillus subtilis NRRL B-209, Citrobacter freundi NRRL B-2643 and Staphylococcus aureus ATCC 29213. Consequently, it is proposed that strain CR3506(T) represents a novel Saccharopolyspora species for which the name Saccharopolyspora hattusasensis sp. nov. is proposed. The type strain is CR3506(T) (=KCTC 29104(T) = DSM 45715(T)).
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    Saccharopolyspora soli sp. nov., isolated from Northern Cyprus soil
    (Springer, 2022) Veyisoglu, Aysel; Tatar, Demet; Saygin, Hayrettin; Cetin, Demet; Guven, Kiymet; Sahin, Nevzat
    A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain K220(T), was isolated from soil collected from Cape Andreas (Zafer Burnu), Northern Cyprus, and subjected to a polyphasic taxonomic approach. The organism was shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Saccharopolyspora. 16S rRNA gene sequence analysis of strain K220(T) showed that it is closely related to the type strains of Saccharopolyspora maritima 3SS5-12 (T), Saccharopolyspora kobensis JCM 9109 (T) and Saccharopolyspora hirsuta ATCC 27875 (T) with 97.6, 97.5 and 97.0% sequence similarity, respectively. In silico DNA-DNA hybridization and average nucleotide identity values between strain K220(T) and type strains of the genus Saccharopolyspora with publicly available genomes were 22.1-31.2% and 76.0-83.16%, respectively. The DNA G + C content of strain K220(T) was 68.3 mol%. The genome of strain K220(T) has genes associated with 24 biosynthetic gene clusters. The strain contained MK-9(H-4) and iso-C-16: 0 as the predominant respiratory quinone and fatty acid, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine. Based on evidence collected from the genotypic, phenotypic and phylogenetic analyses, strain K220(T) is considered to represent a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora soli sp. nov. is proposed. The type strain is K220(T) (= JCM 33912(T) = KCTC 49395(T)).
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    Streptomyces boluensissp. nov., isolated from lake sediment
    (Springer, 2020) Tokatli, Ali; Idil, Onder; Veyisoglu, Aysel; Saygin, Hayrettin; Guven, Kiymet; Cetin, Demet; Sahin, Nevzat
    A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain YC537(T), was isolated from lake sediment collected from Yenicaga Lake, Bolu, Turkey, and subjected to a polyphasic taxonomic approach. The organism had phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genusStreptomyces. 16S rRNA gene sequence analysis of strain YC537(T)showed that it is closely related to the type strain ofStreptomyces ziwulingensisF22(T)(97.9% sequence similarity),Streptomyces tauricusJCM 4837( T)(97.7%) andStreptomyces beijiangensisNBRC 100044( T)(97.6%). The cell wall of the strain containedLL-diaminopimelic acid and the cell-wall sugars were glucose, galactose and ribose. The major phospholipids of strain YC537(T)were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H-6) and MK-9(H-8). The major cellular fatty acids wereiso-C-16:0,iso-C-14:0,anteiso-C(15:0)andiso-C-15:0. Consequently, strain YC537(T)is considered to represent a novel species in the genusStreptomyces, for which the nameStreptomyces boluensissp. nov. is proposed. The type strain is YC537(T)(= KCTC 39750( T) = DSM 102303( T)).
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    Streptomyces boncukensissp. nov., isolated from saltern soil
    (Springer, 2021) Tatar, Demet; Veyisoglu, Aysel; Saygin, Hayrettin; Sahin, Nevzat
    A novel Gram-stain positive, aerobic, non-motile Actinobacterium, designated strain SB3404(T), was isolated from saltern soil collected from Boncuk Saltern, Sungurlu-corum, Turkey, and subjected to a polyphasic taxonomic approach. The organism has shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genusStreptomyces. 16S rRNA gene sequence analysis of strain SB3404(T)showed that it is closely related toStreptomyces albusNBRC 13014(T)(97.2% sequence similarity),Streptomyces xishensisYIM M 10378(T)(96.7%) andStreptomyces abyssalisYIM M 10400(T)(96.5%). The cell wall of the strain containedLL-diaminopimelic acid and the cell-wall sugars were glucose, mannose and ribose. The predominant menaquinones were identified as MK-9(H-8) and MK-9(H-6). The major cellular fatty acids were found to beiso-C-16:0,anteiso-C(17:0)andanteiso-C-15:0. Consequently, strain SB3404(T)is considered to represent a novel species in the genusStreptomyces, for which the nameStreptomyces boncukensissp. nov. is proposed. The type strain is SB3404(T)(= KCTC 49371(T) = JCM 34018(T)).
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    Streptomyces coryli sp. nov., isolated from hazelnut orchard soil
    (Microbiology Soc, 2020) Saygin, Hayrettin; Veyisoglu, Aysel; Tatar, Demet; Nigiz, Cengiz; Tokatli, Ali; Sahin, Nevzat
    A novel actinobacteria, isolate A7024(T), was isolated from commercial hazelnut orchard soil sample which was collected at Duzce, West Black Sea region, Turkey. A polyphasic taxonomic study was carried out to determine the status of this isolate. The phylogenetic tree reconstructed using the neighbour-joining algorithm based on 165 rRNA gene sequences indicated that isolate A7024(T) was positioned within the members of the genus Streptomyces with the highest sequence similarity (97.7%) to Streptomyces cadmiisoli ZFG47(T). The organism formed an extensively branched substrate and aerial hyphae which generated irregular rod-shaped spores with smooth-surfaces. The cell wall of strain A7024(T) contained LL-diaminopimelic. Glucose, mannose and ribose were detected as whole-cell sugars. Its polar lipids were diphosphatidylglycerol. phosphatidylethanol-amine, phosphatidylinositol, three unidentified phospholipids and three unidentified glycolipids. Major menaquinones were MK-9(H-6) and MK-9(H-4). The major cellular fatty acids were iso-C-16:0, anteiso-C-1(5:0) and anteiso-C-1(7:)0. Strain A7024(T) had a genome size of 9.0 Mb with a genome G+C content of 71.5 mol%. The low level of 16S rRNA gene similarity, 19.3 +/- 2.3% digital DNA-DNA-hybridization and 76.94% average nucleotide identity values, as well as some different phenotypic characteristics allowed the strain to be distinguished from the closely related type strains. Therefore, it is concluded that strain A7024(T) represents a novel species of the genus of Streptomyces, for which the name Streptomyces coryli sp. nov. is proposed. The type strain is A7024(T) (=DSM 42066(T)=KCTC 29102(T)=NRRL B-24888(T)).
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    Streptomyces ovatisporus sp nov., isolated from deep marine sediment
    (Microbiology Soc, 2016) Veyisoglu, Aysel; Cetin, Demet; Bektas, Kadriye Inan; Guven, Kiymet; Sahin, Nevzat
    The taxonomic position of a Gram-staining-positive strain, designated strain S4702(T) was isolated from a marine sediment collected from the southern Black Sea coast, Turkey, determined using a polyphasic approach. The isolate was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its classification as representing a member of the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree. S4702(T) was found to be most closely related to the type strains of Streptomyces marinus (DSM 41968(T); 97.8% sequence similarity) and Streptomyces abyssalis (YIM M 10400(T); 97.6 %). 16S rRNA gene sequence similarities with other members of the genus Streptomyces were lower than 97.5 %. DNA-DNA relatedness of S4702 T and the most closely related strain S. marinus DSM 41968 T was 21.0 %. The G+ C content of the genomic DNA was 72.5 mol%. The cell wall of the strain contained L, L-diaminopimelic acid and the cell-wall sugars were glucose and ribose. The major cellular fatty acids were identified as anteiso-C-15 : 0, iso-C-16 : 0, anteiso-C-17 : 0 and iso-C-15 : 0. The predominant menaquinone was MK-9(H8). The polar lipid profile of S4702(T) consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. S4702(T) could be distinguished from its closest phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that S4702(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces ovatisporus sp. nov. is proposed. The type strain is S4702 T (DSM 42103(T) = KCTC 29206(T) = CGMCC 4.7357(T)).