Streptomyces seoulensis sp. nov

Streptomyces apocyni sp. nov., an endogenous actinomycete isolated from Apocynum venetum

A novel actinomycete, designated strain TRM 66233^T, was isolated from Apocynum venetum L. collected from the Xinjiang Uygur Autonomous Region of China and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66233^T with the genus Streptomyces. Strain TRM 66233^T showed a high similarity value to Streptomyces bikiniensis NRRL B-1049^T (98.07 %) based on the 16S rRNA gene phylogenetic tree. The whole-cell sugar pattern of TRM 66233^T consisted of glucose, galactose, mannose and ribose. The predominant menaquinones were MK-9(H₂), MK-9(H₆), MK-9(H₈) and MK-9(H₁₀). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and four unidentified lipids. The major fatty acids were iso-C_15 : 0, anteiso-C_15 : 0, iso-C_16 : 0, C_16 : 0 and iso-C_17 : 0. The G+C content of the DNA was 70.35 mol%. The DNA-DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain TRM 66233^T and closely related type strains were significantly lower than the recommended threshold values. The whole-genome average nucleotide identity and digital DNA-DNA hybridization values between strain TRM 66233^T and S. bikiniensis NRRL B-1049^T were 78.86 and 23.2 %, respectively. On the basis of evidence from this polyphasic study, strain TRM 66233^T should represent a novel species of the genus Streptomyces, for which the name Streptomyces apocyni sp. nov. is proposed. The type strain is TRM 66233^T (=CCTCC AA 2019056^T=LMG 31559^T).

Streptomyces soli sp. nov., isolated from birch forest soil

A Gram-staining positive, aerobic, non-motile, rod-shaped bacterium, designated strain LAM7114^T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, China. The optimal temperature and pH for the growth of strain LAM7114^T were 30 °C and 7.0, respectively. Strain LAM7114^T could grow in the presence of NaCl up to 10% (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that LAM7114^T was closely related to the members of the family genus Streptomyces, with the highest similarity to Streptomyces urticae NEAU-PCY-1^T (98.3%) and Streptomyces fildesensis GW25-5^T (98.2%). The genomic G + C content was 70.0 mol%. The DNA-DNA hybridization values between strain LAM7114^T and S. urticae CCTCC AA 2017015^T, S. fildesensis CGMCC 4.5735^T were 32.5 ± 1.8% and 27.5 ± 2.6%, respectively. The cell wall contained LL-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The whole-cell hydrolysates included glucose and mannose. The major fatty acids were anteiso-C_15:0, iso-C_15:0 and iso-C_16:0. The predominant menaquinones were MK-9(H₆), MK-9(H₄) and MK-9(H₈). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three unidentified aminophospholipids, three unidentified phospholipids, and an unidentified aminolipid. Based on the phenotypic characteristics and genotypic analyses, we propose that strain LAM7114^T represents a novel species in the genus Streptomyces, for which the name Streptomyces soli sp. nov. is proposed. The type strain is LAM7114^T (= CGMCC 4.7581^T = JCM 32822^T).

Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase

BACKGROUND

Streptomyces seoulensis has contributed to the discovery and initiation of extensive research into nickel superoxide dismutase (NiSOD), a unique type of superoxide dismutase found in actinomycetes. Still so far, there is no information about whole genome sequence of this strain.

OBJECTIVE

To investigate complete genome sequence and perform bioinformatic analyses for genomic functions related with nickel-associated genes.

METHODS

DNA was extracted using the Wizard Genomic DNA Purification Kit then sequenced using a Pacific Biosciences SMRT cell 8Pac V3 DNA Polymerase Binding Kit P6 with the PacBiov2 RSII platform. We assembled the PacBio long-reads with the HGAP3 pipeline.

RESULTS

We obtained complete genome sequence of S. seoulensis, which comprises a 6,339,363 bp linear chromosome. While analyzing the genome to annotate the genomic function, we discovered the nickel-associated genes. We observed that the sodN gene encoding for NiSOD is located adjacent to the sodX gene, which encodes for the nickel-type superoxide dismutase maturation protease. In addition, several nickel-associated genes and gene clusters-nickel-responsive regulator, nickel uptake transporter, nickel-iron [NiFe]-hydrogenase and other putative genes were also detected. Strain specific genes were discovered through a comparative analysis of S. coelicolor and S. griseus. Further bioinformatic analyses revealed that this strain encodes at least 22 putative biosynthetic gene clusters, thereby implying that S. seoulensis has the potential to produce novel bioactive compounds.

CONCLUSION

We annotated the genome and determined nickel-associated genes and gene clusters and discovered biosynthetic gene clusters for secondary metabolites implying that S. seoulensis produces novel types of bioactive compounds.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Streptomyces salilacus sp. nov., an actinomycete isolated from a salt lake

The taxonomic position of a novel actinomycete, strain TRM 41337^T, isolated from sediment of a salt lake, Xiaoerkule Lake, Xinjiang, China, was determined by a polyphasic approach. Strain TRM 41337^T grew optimally at 28 °C and in the presence of 1 % (w/v) NaCl. It grew at up to pH 12. The whole-cell sugars of strain TRM 41337^T were ribose and xylose. The diagnostic diamino acid contained ll-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside and two other unidentified phospholipids. The predominant menaquinones were MK-9(H8), MK-9, MK-9(H4) and MK-9(H6). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 1 H. Based on morphological and chemotaxonomic characteristics, the isolate was determined to belong to the genus Streptomyces. The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1498 nt) with representative strains showed that the strain consistently falls into a distinct phyletic lineage together with Streptomyces barkulensis DSM 42082^T (97.48 % similarity) and a subclade consisting of Streptomyces fenghuangensis GIMN 4.003^T (97.20 %), Streptomyces macrosporus NBRC 14748^T (97.14 %) and Streptomyces radiopugnans R97^T (97.01 %). On the basis of these data, strain TRM 41337^T should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces salilacus sp. nov. is proposed. The type strain is TRM 41337^T (=CCTCC AA 2015030^T=KCTC 39726^T).

Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria

To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.

Streptomyces siamensis sp. nov., and Streptomyces similanensis sp. nov., isolated from Thai soils

Three actinomycete strains, KC-038(T), KC-031 and KC-106(T), were isolated from soil samples collected in the southern Thailand. The morphological and chemotaxonomic properties of strains KC-038(T), KC-031 and KC-106(T) were consistent with the characteristics of members of the genus Streptomyces, that is, the formation of aerial mycelia bearing spiral spore chains; the presence of LL-diaminopimelic acid in the cell wall, MK-9 (H6), MK-9 (H4) and MK-9 (H8) as the predominant menaquinones; and C16:0, iso-C16:0 and anteiso-C15:0 as the major cellular fatty acids. 16S rRNA gene sequence analyses indicated that strains KC-038(T) and KC-031 were highly similar (99.9%), and they were closely related to S. olivochromogenes NBRC 3178(T) (98.1%) and S. psammoticus NBRC 13971(T) (98.1%). Strain KC-106(T) was closely related to S. seoulensis NBRC 16668(T) (98.9%), S. recifensis NBRC 12813(T) (98.9%), S. chartreusis NBRC 12753(T) (98.7%) and S. griseoluteus NBRC 13375(T) (98.4%). The values of DNA-DNA relatedness between the isolates and the type strains of the related species were below 70%. On the basis of the polyphasic evidence, the isolates should be classified as two novel species, namely Streptomyces siamensis sp. nov. (type strain, KC-038(T) = NBRC 108799(T) = PCU 328(T) = TISTR 2107(T)) and Streptomyces similanensis sp. nov. (type strain, KC-106(T) = NBRC 108798(T) = PCU 329(T) = TISTR 2104(T)).

Streptomyces aidingensis sp. nov., an actinomycete isolated from lake sediment

A novel actinomycete strain, designated TRM 46012(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The strain was aerobic and Gram-staining-positive with an optimum NaCl concentration for growth of 0-5% (w/v). The isolate had sparse aerial mycelium and produced bud-shaped spores at the end of the aerial mycelium on ISP medium 4. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and three unidentified glycolipids. The predominant menaquinones were MK-9(H₆), MK-9(H₈) and MK-9(H₄). The major fatty acids were iso-C(16:0), anteiso-C(17:0) and anteiso-C(15:0). The G+C content of the DNA was 74.4 mol%. Phylogenetic analysis showed that strain TRM 46012(T) had 16S rRNA gene sequence similarity of 95.7% with the most closely related species with a validly published name, Streptomyces cheonanensis, and it could be distinguished from all species in the genus Streptomyces by using the data from this polyphasic taxonomic study. On the basis of these data, strain TRM 46012(T) should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces aidingensis sp. nov. is proposed. The type strain is TRM 46012(T) ( =CGMCC 4.5739(T) =NBRC 108211(T)).

Streptomyces wuyuanensis sp. nov., an actinomycete from soil

A novel actinomycete, strain FX61(T), was isolated from a saline sample collected from the Inner Mongolian Autonomous Region in China and subjected to a taxonomic study using a polyphasic approach. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 1 H, C16 : 0, iso-C14 : 0 and anteiso-C17 : 0. The phospholipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides and an unidentified phospholipid. The G+C content of the genomic DNA was 72 mol%. The 16S rRNA gene sequence of the isolate had greater than 98 % similarity with those of Streptomyces griseoincarnatus ATCC 23623(T) (98.2 %), Streptomyces labedae DSM 41446(T) (98.2 %), Streptomyces variabilis ATCC 19815(T) (98.2 %), Streptomyces erythrogriseus ATCC 27427(T) (98.2 %), Streptomyces matensis ATCC 23935(T) (98.2 %), Streptomyces althioticus ATCC 19724(T) (98.2 %) and Streptomyces luteosporeus ATCC 33049(T) (98.0 %), showing that the novel strain should be assigned to the genus Streptomyces. DNA-DNA hybridizations with the seven above-mentioned members of the genus Streptomyces showed 29.8, 28.5, 27.0, 25.5, 25.0, 23.5 and 22.0 % relatedness, respectively. On the basis of the phenotypic characteristics and genotypic distinctiveness, strain FX61(T) should be classified as a novel species of the genus Streptomyces, for which the name Streptomyces wuyuanensis sp. nov. is proposed. The type strain is FX61(T) (= CGMCC 4.7042(T) = KCTC 29112(T)).

Antibiofilm activity of Streptomyces sp. BFI 230 and Kribbella sp. BFI 1562 against Pseudomonas aeruginosa

Members of the actinomycetes family are a rich source of bioactive compounds including diverse antibiotics. This study sought to identify novel and non-toxic biofilm inhibitors from the actinomycetes library for reducing the biofilm formation of Pseudomonas aeruginosa PAO1. After the screening of 4104 actinomycetes strains, we found that the culture spent medium (1 %, v/v) of Streptomyces sp. BFI 230 and Kribbella sp. BFI 1562 inhibited P. aeruginosa biofilm formation by 90 % without affecting the growth of planktonic P. aeruginosa cells, while the spent media enhanced the swarming motility of P. aeruginosa. Global transcriptome analyses revealed that the spent medium of Streptomyces sp. BFI 230 induced expression of phenazine, pyoverdine, pyochelin synthesis genes, and iron uptake genes in P. aeruginosa. The addition of exogenous iron restored the biofilm formation and swarming motility of P. aeruginosa in the presence of the spent medium of Streptomyces sp. BFI 230, which suggests that the Streptomyces sp. BFI 230 strain interfered iron acquisition in P. aeruginosa. Experiments on solvent extraction, heat treatment, and proteinase K treatment suggested that hydrophilic compound(s), possibly extracellular peptides or proteins from Streptomyces sp. BFI 230 cause the biofilm reduction of P. aeruginosa. Together, this study indicates that actinomycetes strains have an ability to control the biofilm of P. aeruginosa.

From bulk to single-cell classification of the filamentous growing Streptomyces bacteria by means of Raman spectroscopy

Classification of Raman spectra recorded from single cells is commonly applied to bacteria that exhibit small sizes of approximately 1 to 2 μm. Here, we study the possibility to adopt this classification approach to filamentous bacteria of the genus Streptomyces. The hyphae can reach extensive lengths of up to 35 μm, which can correspond to a single cell identified in light microscopy. The classification of Raman bulk spectra will be demonstrated. Here, ultraviolet resonance Raman (UV RR) spectroscopy is chosen to classify six Streptomyces species by the application of a tree-like classifier. For each knot of the hierarchical classifier, estimated classification accuracies of over 94% are accomplished. In contrast to the classification of bulk spectra, the classification of single-cell spectra requires a homogenous substance distribution within the cell. Consequently, the bacterial cell chemistry can be represented by one individual spectrum. This requirement is not fulfilled when different spectra are processed from different locations within the cell. Bacteria of the investigated genus Streptomyces exhibit, besides the normal bacterial spectra, lipid-rich spectra. The occurrence of lipid enrichment depends on culture age and nutrition availability. With this study, we investigate the cell substance distribution, especially of lipid-rich fractions. The classification utilizing a tree-like classifier is also applied to the Streptomyces single-cell spectra, resulting in classification accuracies between 80 and 93% for the investigated Streptomyces species.

Streptomyces fildesensis sp. nov., a novel streptomycete isolated from Antarctic soil

A novel actinomycete strain, GW25-5(T), was isolated from a soil sample collected from the Fildes Peninsula, King George Island, West Antarctica. The strain was characterized by white to grey aerial mycelia, which were differentiated to straight to flexuous spore chains, with rod-shaped smooth spores. The cell wall of strain GW25-5(T) contained LL-diaminopimelic acid (A(2)pm) and traces of meso-A(2)pm. Whole-cell sugars were galactose and minor amounts of mannose and glucose. The predominant menaquinones were MK-9(H(6)) (49%), MK-9(H(8)) (24%) and MK-9(H(4)) (12%). The phospholipids contained DPG, PE, PI, PIM and PL(s). The major cellular fatty acids were iso-C(16:0) and anteiso-C(15:0). Genomic DNA G+C content of strain GW25-5(T) was 70.0 mol%. BLAST result showed that strain GW25-5 has the 16S rRNA gene sequence highest similarity of 97.5% with members of genus Streptomyces and phylogenetic analysis indicated that this strain belongs to the genus Streptomyces. DNA-DNA relatedness values of strain GW25-5(T) with the closest species of Streptomyces purpureus LMG 19368(T) and Streptomyces beijiangensis YIM 6(T) were significantly lower than 70% of the threshold value for the delineation of genomic species. A polyphasic taxonomic investigation based on a judicious combination of genotypic and phenotypic characteristics revealed that the organism represents a novel species of the genus Streptomyces. Thus, we propose strain GW25-5(T) as the type strain of this novel species, Streptomyces fildesensis (=CGMCC 4.5735(T) = YIM 93602(T) = DSM 41987(T) = NRRL B 24828(T)).

Streptomyces qinglanensis sp. nov., isolated from mangrove sediment

A Streptomyces-like strain, 172205(T), was obtained from mangrove soil collected at Qinglan Harbour, Wenchang, Hainan, China. The strain was characterized by white aerial mycelium and long spore chains. Comparison of 16S rRNA gene sequences indicated that the strain represents a novel member of the genus Streptomyces, exhibiting highest levels of similarity (<98.29%) to the type strains of members of the genus Streptomyces. However, DNA-DNA relatedness and phenotypic data readily distinguished strain 172205(T) from phylogenetically related type strains. The predominant menaquinones were MK-9(H(6)) and MK-9(H(8)). The major fatty acids were iso-C(15:0) (10.31%), anteiso-C(15:0) (35.19%), iso-C(16:0) (20.24%) and anteiso-C(17:0) (10.05%). The diagnostic phospholipid was phosphatidylethanolamine. The cell wall contained ll-diaminopimelic acid and meso-diaminopimelic acid and whole-cell hydrolysates contained ribose, galactose and glucose. The results of DNA-DNA hybridization, physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 172205(T) from phylogenetically related type strains. Therefore, strain 172205(T) is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces qinglanensis sp. nov. is proposed. The type strain is 172205(T) (=CGMCC 4.6825(T) =DSM 42035(T)).

Streptomyces artemisiae sp. nov., isolated from surface-sterilized tissue of Artemisia annua L

The taxonomic position of an actinomycete strain YIM 63135(T), which was isolated from the surface-sterilized tissue of Artemisia annua L. collected from Yunnan province, south-west China, was determined by using a polyphasic approach. Morphological and chemical characteristics of the novel strain were consistent with those of the genus Streptomyces. It developed a pinkish aerial mycelium and pinkish-brown substrate mycelium on oatmeal agar. The cell wall of the strain contained ll-diaminopimelic acid. The menaquinones comprised MK-9(H(6)) (62.8 %), MK-9(H(8)) (31.4 %) and MK-9(H(4)) (5.9 %). The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, an unknown glucosamine-containing phospholipid (GluNu), phosphatidylinositol mannosides and four unknown ninhydrin-negative phospholipids. The major fatty acids were iso-C(16 : 0) (30.0 %), anteiso-C(17 : 0) (27.3 %) and anteiso-C(15 : 0) (17.0 %). The DNA G+C content of strain YIM 63135(T) was 72.6 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain YIM 63135(T) is a member of the genus Streptomyces and exhibited 99.9 % gene sequence similarity to Streptomyces armeniacus NBRC 12555(T), while low sequence similarity values (<97.0 %) distinguished strain YIM 63135(T) from all other Streptomyces species. DNA-DNA hybridization studies suggested that strain YIM 63135(T) represents a different genomic species. On the basis of phenotypic and phylogenetic characteristics, strain YIM 63135(T) was considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces artemisiae sp. nov. is proposed, with YIM 63135(T) (=CCTCC AA 208059(T) =DSM 41953(T)) as the type strain.

Streptomyces thinghirensis sp. nov., isolated from rhizosphere soil of Vitis vinifera

A novel actinomycete, strain S10(T), was isolated from rhizosphere soil of wild Vitis vinifera in Thinghir, Ouarzazate Province, Southern Morocco. The taxonomic status of this strain was established using a polyphasic approach. Strain S10(T) had white-grey aerial mycelium with long, spiral spore chains bearing smooth surfaced spores and produced a yellow diffusible pigment. Chemotaxonomic analyses showed that the cell wall of strain S10(T) contained ll-diaminopimelic acid and glycine. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that strain S10(T) belonged to the Group I streptomycetes, branching off next to Streptomyces marokkonensis LMG 23016(T) from the Streptomyces violaceoruber group. DNA-DNA relatedness and phenotypic data distinguished strain S10(T) from the phylogenetically closest related type strains. It is therefore proposed that strain S10(T) (=CCMM B35(T)=DSM 41919(T)) represents the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces thinghirensis sp. nov. is proposed.

Streptomyces mayteni sp. nov., a novel actinomycete isolated from a Chinese medicinal plant

An actinomycete strain, designated YIM 60475(T), was isolated from the roots of Maytenus austroyunnanensis and was characterized by using a polyphasic approach. The strain was determined to belong to the genus Streptomyces, based on its phenotypic and phylogenetic characteristics. The strain produced spiral spore chains on aerial mycelium. The cell wall contained LL-diaminopimelic acid. Whole-cell hydrolysates contained galactose, glucose, and xylose. The phospholipid was type II. The DNA G+C content of the type strain was 73.3 mol%. DNA-DNA hybridization and comparison of physiological and chemical characteristics suggested that strain YIM 60475(T) is a new Streptomyces species, for which the name Streptomyces mayteni sp. nov. is proposed. The type strain is YIM 60475(T) (=CCTCC AA 207005(T) = KCTC 19383(T)).

Streptomyces durmitorensis sp. nov., a producer of an FK506-like immunosuppressant

Screening of soil samples from the Durmitor National Park, Serbia and Montenegro, for strains producing immunosuppressants with a similar mechanism of action to FK506 resulted in the isolation of the actinomycete strain MS405T. Isolate MS405T was found to have morphological and phenotypic properties that were consistent with its classification as a Streptomyces strain. The DNA G+C content of strain MS405T was 72 mol%. 16S rRNA gene sequence data confirmed the taxonomic position of the strain, following the generation of phylogenetic trees by using various treeing algorithms. On the basis of 16S rRNA gene sequence similarity, strain MS405T was shown to belong to the Streptomyces albidoflavus ‘supercluster’, being related to Streptomyces aureus DSM 41785T (99.59 % similarity) and Streptomyces kanamyceticus DSM 40500T (99.32 %). The 16S–23S rRNA internally transcribed spacer (ITS) region exhibited variations in length and sequence composition, showing limited usefulness in phylogenetic analyses. However, DNA relatedness values support the classification of this isolate within a novel species. A number of physiological and biochemical tests distinguished strain MS405T from its closest phylogenetic neighbours. Therefore, strain MS405T represents a novel species, for which the name Streptomyces durmitorensis sp. nov. is proposed, with the type strain MS405T (=DSM 41863T =CIP 108995T).

Biologically active endophytic streptomycetes from Nothofagus spp. and other plants in Patagonia

Endophytic streptomycetes have been isolated and characterized from several species of Nothofagus and other plants growing in the southern reaches of Patagonia. No endophytic streptomycete was obtained from any plant species studied in Northern Patagonia. However, from Southern Patagonia, biologically active Streptomyces spp. from several plant species were isolated. Each isolate, as studied by scanning electron microscopy (SEM), has small hyphae, some produce typical barrel-shaped spores in culture and each has some unique hyphal surface structures. Interestingly, although none has any detectable antibacterial killing properties, each has demonstrable killing activity against one or more pathogenic fungi including representative plant pathogenic organisms such as Phytophthora erythroseptica, Pythium ultimum, Sclerotinia sclerotiorum, Mycosphaerella fijiensis, and Rhizoctonia solani. The 16S rDNA sequences of the isolates were distinct from all other genetic accessions of Streptomyces in GenBank. However, isolate C-2 from Chiliotrichum diffusum (Compositae) is identical, in all respects, to isolate C-4 obtained from Misodendrum punctulatum (Loranthaceae). These results confirm that endophytic streptomycetes represent a novel source of biologically active microorganisms.

Streptomyces gulbargensis sp. nov., isolated from soil in Karnataka, India

During the course of screening for industrially important microorganisms, an alkali-tolerant and thermotolerant actinomycete, strain DAS 131T, was isolated from a soil sample collected from the Gulbarga region, Karnataka province, India. The strain was characterized by a polyphasic approach that showed that it belonged to the genus Streptomyces. Growth was observed over a wide pH range (pH 6-12) and at 45 degrees C. The 16S rRNA gene sequence of strain DAS 131T was deposited in the GenBank database under the accession number DQ317411. 16S rRNA gene sequence analysis revealed that strain DAS 131T was most closely related to Streptomyces venezuelae ISP 5230T (AY999739) with a sequence similarity of 99.5% (8 nucleotide differences out of 1,477). Despite this very high sequence similarity, strain DAS 131T was phenetically distinct from S. venezuelae. The DNA relatedness between these strains was 54%, indicating that strain DAS 131T is a distinct genomic species. On the basis of phenetic and genetic analyses, strain DAS 131T is classified as a new species in the genus Streptomyces, for which we propose the name Streptomyces gulbargensis sp. nov.

Streptomyces cheonanensis sp. nov., a novel streptomycete with antifungal activity

Actinomycete strain VC-A46T, which exhibits antifungal activity, was isolated from a soil sample collected from Cheonan, Korea. The strain was determined to belong to the genus Streptomyces, based on its morphological and chemotaxonomic characteristics. The cell wall of this strain contained ll-diaminopimelic acid. The predominant fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 cis 9. The DNA G+C content of strain VC-A46T was 75·5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of this strain revealed that it differed from those of the described streptomycetes available in public databases. Analyses of DNA–DNA relatedness data, together with data regarding the strain's morphological, physiological and biochemical characteristics, also confirmed that this strain constitutes a novel Streptomyces taxon, which is distinguishable from closely related reference strains. Therefore, it is proposed that strain VC-A46T (=KCCM 42119T=NBRC 100940T) represents the type strain of a novel species, named Streptomyces cheonanensis sp. nov.

Streptomyces daliensis sp. nov. from soil

A novel actinomycete strain YIM 31724(T) was isolated from a soil sample collected from Dali, Yunnan Province, People's Republic of China. The strain is characterized by white to yellow white aerial mycelia, spiral spore chains and smooth spore surface. The cell wall of strain YIM 31724(T) contained LL-diaminopimelic acid (A(2)pm) and traces of meso-A(2)pm. Whole-cell hydrolysates contained mainly glucose and small amounts of galactose and xylose. The menaquinones were MK-9(H(6)) (31%) and MK-9(H(8)) (69%). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 31724(T) was 67.2 mol%. Phylogenetic analysis indicated that the strain belongs to the genus Streptomyces, with highest similarity to Streptomyces rimosus subsp. rimosus JCM 4667(T) (rRNA gene sequence similarity value of 98.9%) and Streptomyces erumpens DSM 40941(T) (rRNA gene sequence similarity value of 98.7%). Based on its phenotypic and genotypic characteristics, including low DNA-DNA hybridization results, strain YIM 31724(T)(= CCTCC AA204020(T) = KCTC 19076(T)) is proposed as the type strain of a novel species, Streptomyces daliensis sp. nov.

Streptomyces roseoalbus sp. nov., an actinomycete isolated from soil in Yunnan, China

An actinomycete strain was isolated from a soil sample collected from a secondary forest at Yongsheng of Yunnan province, China. The isolate, YIM 31634T, was identified by a polyphasic approach. The 16S rDNA sequence analysis showed that the strain YIM 31634T belongs to the genus Streptomyces, with closest similarity to Streptomyces olivochromogenes DSM 40451T (97.66% similarity). Sequence similarities between strain YIM 31634T and other Streptomyces species in the same subclade ranged from 97.59% (with Streptomyces resistomycificus DSM 40133T) to 97.22% (with Streptomyces mirabilis ATCC 27447T). Key phenotypic characteristics as well as chemotaxonomic features of the actinomyces were congruent with the description of the genus Streptomyces. On the basis of phenotypic and phylogenetic analyses, strain YIM31634T was recognized as a new species of the genus Streptomyces for which the name Streptomyces roseoalbus sp. nov. is proposed. The strain YIM 31634T has been deposited in the Chinese Center of Type Culture Collection as strain CCTCC M 203016T and in the Deutsche Sammlung von Mikroorganismen (DSM 41833T).

Crystal structure of nickel-containing superoxide dismutase reveals another type of active site

Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.

Streptomyces hebeiensis sp. nov

A novel actinomycete strain, YIM 001T, was isolated from a soil sample collected from Hebei province, People's Republic of China. The strain was characterized by white to grey aerial mycelium. Long spore chains, borne on the aerial mycelium, were straight to Rectiflexibiles; the spore chains were composed of non-motile and coccoid spores with a warty surface. The cell wall of strain YIM 001T contained ll-diaminopimelic acid (A2pm) and traces of meso-A2pm. Whole-cell hydrolysates contained mainly glucose and small amounts of xylose, galactose and arabinose. The menaquinones were MK-9(H4) (4·6 %), MK-9(H6) (60 %), MK-9(H8) (30·7 %) and MK-9(H10) (4·7 %). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 001T was 71·4 mol%. Phylogenetic analysis indicated that strain YIM 001T belongs to the genus Streptomyces. Based on its phenotypic and genotypic characteristics, strain YIM 001T (=CCTCC AA 203005T=CIP 107974T=DSM 41837T) is proposed as the type strain of a novel species, Streptomyces hebeiensis sp. nov.

CbiX-homologous protein (CbiXhp), a metal-binding protein, fromStreptomyces seoulensisis involved in expression of nickel-containing superoxide dismutase

To find the accessory proteins participating in expression and maturation of nickel-containing superoxide dismutase (NiSOD), a metal-binding protein (CbiXhp) homologous to cobaltochelatase (CbiX) of Bacillus megaterium was isolated by nickel-nitrilotriacetic acid resin from Streptomyces seoulensis. The deduced amino acid sequence of cbiXhp showed 87% and 39% identity to CbiX of Streptomyces coelicolor and that of B. megaterium, respectively. Overexpression of CbiXhp increased the activity and the expression of NiSOD in the presence and absence of nickel, but to a lesser extent in its absence. This result indicates that CbiXhp is involved in the expression of NiSOD.

Properties of purified cytosolic isoenzyme I of Cu,Zn-superoxide dismutase from Nicotiana plumbaginifolia leaves

The isoenzyme I of cytosolic Cu,Zn-superoxide dismutase (SOD) from Nicotiana plumbaginifolia (tobacco) leaves has been purified to apparent homogeneity. The relative molecular mass of the native isoenzyme, determined by gel filtration chromatography, is about 33.2 kDa. SDS-polyacrylamide gel electrophoresis shows that the enzyme is composed of two equal subunits of 16.6 kDa The isolectric point, assayed by isoelectric focusing, in the pH range of 3.5-6.5, is 4.3. The enzyme stability was tested at different temperatures, pH, and concentration of inhibitors (KCN and H(2)O(2)). The catalytic constant (k(cat)) was 1.17 +/- 0.14 x 10(9) M(-1) s(-1) at pH 9.9 and 0.1 M ionic strength. The activation energy of the thermal denaturation process is 263 kJ mol(-1). The electrostatic surface potential of the modeled tobacco Cu,Zn-SOD I was calculated showing that the functional spatial network of charges on the protein surface has been maintained, independently of the amino acid substitution around the active sites.

Duplicate genes for Fe-containing superoxide dismutase in Streptomyces coelicolor A3(2)

Streptomyces coelicolor Müller contains two types of superoxide dismutase (SOD) containing Ni (encoded by sodN) or Fe (encoded by sodF). Unlike a single species of Fe-containing SOD in Müller strain, multiple forms of FeSODs were detected in S. coelicolor A3(2) strain by activity staining and Western blot analysis. Genomic Southern hybridization suggested the presence of at least two copies of the sodF-like gene in A3(2). Two different genes for FeSOD (sodF1 and sodF2) were isolated from the phage library of A3(2) genome. The nucleotide sequence of the sodF1 coding region was identical with the unique sodF gene from Müller while that of sodF2 shared 88% identity. The gene products of sodF1 and sodF2 were identified by activity staining and immunoblot analysis. Expression from the sodF1 gene was repressed by nickel as sensitively as Müller sodF, suggesting the presence of Ni-responsive regulatory site within the region shared by the two genes. Among 12 other Streptomyces species examined, only S. fradiae contained two FeSOD-like polypeptides. We postulate that the additional copy of the sodF gene (sodF2) was provided by the horizontal transfer from remotely related bacteria.

Structure/function relationships in nickel metallobiochemistry

Among the many highlights of nickel metallobiochemistry in 1998 were the discoveries that Escherichia coli glyoxalase I is the first example of a nickel isomerase, and that the superoxide dismutase isolated from Streptomyces seoulensis is a new structural class of superoxide dismutase that features thiolate ligation.

Lipoamide dehydrogenase from streptomyces seoulensis: biochemical and genetic properties

Lipoamide dehydrogenase was purified around 22-fold relative to the crude extracts of Streptomyces seoulensis with an overall yield of 9. 5%. The enzyme was composed of two identical subunits with a molecular mass of 54 kDa and contained 1 mol of FAD per mol of subunit. The absorption spectra of the enzyme revealed the absorption maxima of flavoprotein at 272, 349, and 457 nm. Catalytically active two-electron reduced lipoamide dehydrogenase was produced by anaerobic reduction with one equivalent of NADH. Addition of excess amount of NADH led to the four-electron reduced lipoamide dehydrogenase. The reaction of the enzyme in the reduction reaction of lipoamide or lipoic acid could be explained by a ping-pong mechanism like many other lipoamide dehydrogenases reported earlier. The enzyme also catalysed the reduction of various quinone compounds with NADH as electron donor via a ping-pong mechanism. The enzyme can catalyse a single electron transfer in case of quinone-reducing process, evidenced by the production of 1, 4-naphthosemiquinone radical anion. The quinone-reducing activity of the enzyme was dramatically inhibited by NAD+, indicating the involvement of four-electron reduced form. The structural gene for the enzyme was cloned using a DNA fragment PCR-amplified with the primers designed from N-terminal and internal amino acid sequences. The deduced amino acid sequence shared striking similarity with those of lipoamide dehydrogenases from prokaryotes and eukaryotes. The gene was named lpd. All tested Streptomyces contained one homologue of the lpd gene, which is consistent with the fact that most organisms contain only one lipoamide dehydrogenase.