Nevzat Sahin

Analysis of Thermophilic Clades within the Genus Streptomyces by 16s Ribosomal DNA Sequence Comparisons

Almost complete sequences of the 16S rRNA genes of eight representative thermophilic streptomycetes were determined following the isolation and cloning of the amplified genes. These sequences were aligned with those of representative mesophilic streptomycetes, and phylogenetic trees were inferred by using four tree-making algorithms. The thermophilic streptomycetes formed two distinct clades that were supported by high bootstrap values based on 1,000 resamplings. One clade encompassed Streptomyces macrosporus and related species, and the second clade included Streptomyces thermodiastaticus and allied taxa. The relationships between the organisms were not markedly influenced by the different tree-making methods, but the rooting of the tree was sensitive to the choice of the outgroup strain. It is evident from this study that the thermophilic streptomycetes do not merit recognition as a distinct taxon within the genus Streptomyces.

Classification of thermophilic streptomycetes, including the description of Streptomyces thermoalcalitolerans sp. nov.

A polyphasic taxonomic study was undertaken to clarify relationships within and between representative thermophilic alkalitolerant streptomycetes isolated from soil and appropriate marker strains. The resultant data, notably those from DNA-DNA relatedness studies, support the taxonomic integrity of the validly described species Streptomyces thermodiastaticus, Streptomyces thermoviolaceus and Streptomyces thermovulgaris. However, the genotypic and phenotypic data clearly show that Streptomyces thermonitrificans Desai and Dhala 1967 and S. thermovulgaris (Henssen 1957) Goodfellow et al. 1987 represent a single species. On the basis of priority, S. thermonitrificans is a later subjective synonym of S. thermovulgaris. Similarly, 10 out of the 11 representative thermophilic alkalitolerant isolates had a combination of properties consistent with their classification as S. thermovulgaris. The remaining thermophilic alkalitolerant isolate, Streptomyces strain TA56, merited species status. The name Streptomyces thermoalcalitolerans sp. nov. is proposed for this strain. A neutrophilic thermophilic isolate, Streptomyces strain NAR85, was identified as S. thermodiastaticus.

Optimization of extracellular endoxylanase, endoglucanase and peroxidase production by Streptomyces sp. F2621 isolated in Turkey

Aims:  To determine the effect of environmental conditions on the production of extracellular lignocellulose‐degrading enzymes by Streptomyces sp. F2621 and to assess the potential use of these enzymes in the hydrolysis of lignocellulose material.

Amycolatopsis eurytherma sp. nov., a thermophilic actinomycete isolated from soil

The taxonomic positions of two thermophilic actinomycetes isolated from soil were established in a polyphasic taxonomic study. The organisms were shown to have phenotypic properties typical of members of the genus Amycolatopsis and formed a distinct phyletic line in the Amycolatopsis methanolica 16S rDNA subclade. They also had many phenotypic properties in common and formed a genomic species that was closely related to, albeit distinct from, the type strain of A. methanolica. A range of phenotypic properties distinguished the isolates from representatives of all validly described species of Amycolatopsis. Genotypic and phenotypic data show that the two strains should be classified in the genus Amycolatopsis as a novel species, Amycolatopsis eurytherma sp. nov.; the type strain is strain NT202T (= DSM 44348T = NCIMB 13795T).

Streptomyces hoynatensis sp. nov., isolated from deep marine sediment.

A novel actinobacterium, strain S1412(T), was isolated from a deep sediment sample, collected from the southern Black Sea coast of Turkey, and was examined using a polyphasic approach. The organism had chemical and morphological features typical of the genus Streptomyces. The cell wall of the novel strain contained ll-diaminopimelic acid. Whole-cell hydrolysates contained galactose, glucose and traces of xylose. The polar lipid profile of S1412(T) consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine and phosphatidylinositol, and minor amounts of phosphatidylglycerol. Strain S1412(T) exhibited an unusual quinone system, with the predominant compounds MK-10(H8), MK-9(H8) and MK-10(H6) and small amounts of MK-9(H6) and MK-10(H4). Major fatty acids were iso-C16 : 0, iso-C16 : 1 H and anteiso-C17:0. The 16S rRNA gene sequence similarities for strain S1412(T) with respect to the most closely related type strains of species of the genus Streptomyces were less than 97.0%. Phenotypic data clearly distinguished the isolate from its closest relatives, Streptomyces specialis GW 41-1564(T), Streptomyces mayteni YIM 60475(T), Streptomyces hainanensis YIM 47672(T), Streptomyces avicenniae MCCC1A01535(T) and Streptomyces sedi YIM 65188(T). Based on chemotaxonomic, phenotypic and genotypic characteristics, strain S1412(T) is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces hoynatensis sp. nov. is proposed. The type strain is S1412(T) ( = KCTC 29097(T) = DSM 42069(T)).

Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine.

A novel halotolerant actinomycete, designated strain BNT52(T), was isolated from soil collected from Cihanbeyli Salt Mine in the central Anatolia region of Turkey, and examined using a polyphasic taxonomic approach. The isolate was found to have chemical and morphological properties typical of the genus Amycolatopsis and formed a distinct phyletic line in the 16S rRNA gene tree. Strain BNT52(T) was most closely related to Amycolatopsis nigrescens CSC17Ta-90(T) (96.7 %), Amycolatopsis magusensis KT2025(T) (96.6 %), Amycolatopsis sulphurea DSM 46092(T) (96.6 %), Amycolatopsis dongchuanensis YIM 75904(T) (96.5 %), Amycolatopsis ultiminotia RP-AC36(T) (96.4 %) and Amycolatopsis sacchari DSM 44468(T) (96.4 %). Sequence similarities with other strains of species of the genus Amycolatopsis were lower than 96.2 %. The isolate grew at 20-37 °C, pH 6-12 and in the presence of 0-10 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids were iso-C16 : 0 2-OH and iso-C16 : 0. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylmethylethanolamine. The genomic DNA G+C content was 68.8 mol%. On the basis of the data from this polyphasic taxonomic study, strain BNT52(T) represents a novel species within the genus Amycolatopsis for which the name Amycolatopsis cihanbeyliensis sp. nov. is proposed (type strain BNT52(T) = KCTC 29065(T) = NRRL B-24886(T) = DSM 45679(T)).

Production and partial characterization of extracellular peroxidase produced byStreptomyces sp. F6616 isolated in Turkey

Streptomyces sp. F6616 was found to produce higher levels of extracellular peroxidase activity (0.535 U/mL) without any inducers than other actinobacteria which are previously reported. Maximum specific peroxidase activity (6.21 U/mg of protein) was obtained after 72 h of incubation at 30°C in a minimal salt medium (pH 8.0) containing (in wt/v) 0.6% yeast extract and 0.8% ball-milled wheat straw corresponding to a C:N ratio of 4.6:1. Characterization of the peroxidase revealed that the optimal temperature for the enzyme activity, using the standard 2,4-dichlorophenol (2,4-DCP) assay was 50°C, when the enzyme reaction was performed at pH 8.0. A study of the effect of temperature on the stability of peroxidase over time, showed that the enzyme was stable at 50°C, with a half-life of 145 min, while at higher temperature the stability and activity was reduced such that at 60°C the half-life of the enzyme was 30 min. The optimum pH for the activity of the enzyme occurred between pH 9.0 and 10.0. The apparentKm andVmax values for the peroxidase preparations were determined to be 1.52 mmol/L and 1.84 U/mg protein, respectively using 2,4-DCP as a substrate. Characterization of the peroxidase activity revealed activity against 2,4-DCP, L-3,4-dihydroxyphenylalanine (L-DOPA), 2,4,5-trichlorophenol and other chlorophenols in the presence of hydrogen peroxide. However, inhibition of peroxidase activity with the addition of potassium cyanide and sodium azide, suggested the presence of heme component in the tertiary structure of the enzyme.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Methylobacterium tarhaniae sp. nov., isolated from arid soil.

A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211(T), isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211(T) belonged to the genus Methylobacterium. Strain N4211(T) was most closely related to Methylobacterium aquaticum GR16(T) (98.56 %), Methylobacterium platani PMB02(T) (97.95 %) and Methylobacterium variabile GR3(T) (97.2 %), and the phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C18 : 1 cis11/t9/t6). The DNA G+C content was 67.3 mol%. DNA-DNA relatedness of strain N4211(T) and the most closely related strains M. aquaticum DSM 16371(T) and M. platani KCTC 12901(T) were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA-DNA hybridization data, strain N4211(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium tarhaniae sp. nov. is proposed. The type strain is N4211(T)( = KCTC 23615(T) = DSM 25844(T)).

Saccharomonospora amisosensis sp. nov., isolated from deep marine sediment

A novel actinomycete, strain DS3030(T), was isolated from a deep sediment sample, collected from the southern Black Sea coast, Turkey, and was examined using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain DS3030(T) was shown to belong to the genus Saccharomonospora and to be related most closely to Saccharomonospora marina XMU15(T) (99.6 % similarity). Sequence similarities with other strains of the genus Saccharomonospora were lower than 97.0 %. The organism had chemical and morphological features typical of the genus Saccharomonospora. The cell wall of the novel strain contained meso-diaminopimelic acid, arabinose and galactose as diagnostic sugars. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone was MK-9(H4). Major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH and C16 : 1cis 9. Phenotypic data clearly distinguished the new isolate from its closest relative, S. marina XMU15(T). The combined genotypic and phenotypic data and low DNA-DNA relatedness with its closest related strain reveal that strain DS3030(T) represents a novel species of the genus, for which the name Saccharomonospora amisosensis sp. nov. is proposed. The type strain is DS3030(T) ( = DSM 45685(T) = KCTC 29069(T) = NRRL B-24885(T)).