Hairong He

Streptomyces harbinensis sp. nov., an endophytic, ikarugamycin-producing actinomycete isolated from soybean root [Glycine max (L.) Merr].

A novel ikarugamycin-producing actinomycete, designated strain NEAU-Da3(T), was isolated from soybean root [Glycine max (L.) Merr.] and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-Da3(T) belonged to the genus Streptomyces, and was most closely related to Streptomyces carpaticus NRRL B-16359(T) (99.5 %), Streptomyces cheonanensis VC-A46(T) (99.3 %) and Streptomyces xiamenensis MCCC 1A01550(T) (97.2 %); similarities to other type strains of species of the genus Streptomyces were lower than 97.1 %. The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with S. carpaticus NRRL B-16359(T), S. cheonanensis VC-A46(T) and S. xiamenensis MCCC 1A01550(T). This branching pattern was also supported by the tree reconstructed with the neighbour-joining method. A comparative study between strain NEAU-Da3(T) and the type strains of the closest related species of the genus Streptomyces revealed that it differed from them in morphological, physiological and biochemical characteristics. Therefore, it is proposed that strain NEAU-Da3(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces harbinensis sp. nov. is proposed. The type strain is NEAU-Da3(T) ( = CGMCC 4.7047(T) = DSM 42076(T)).

Streptomyces zhaozhouensis sp. nov., an actinomycete isolated from candelabra aloe (Aloe arborescens Mill).

A novel endophytic actinomycete, designated strain NEAU-LZS-5(T), was isolated from the leaf of candelabra aloe (Aloe arborescens Mill) and characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that strain NEAU-LZS-5(T) belongs to the genus Streptomyces and exhibited 99.51 and 97.37 % similarity to Streptomyces sedi YIM 65188(T) and Streptomyces specialis GW41-1564(T), respectively, whereas low similarity values (<97 %) distinguished strain NEAU-LZS-5(T) from all other species of the genus Streptomyces with validly published names. Two tree-making algorithms also supported the position that strain NEAU-LZS-5(T) formed a distinct clade with Streptomyces sedi YIM 65188(T) and Streptomyces specialis GW41-1564(T). However, levels of DNA-DNA relatedness between strain NEAU-LZS-5(T) and Streptomyces sedi YIM 65188(T) and Streptomyces specialis GW41-1564(T) were 45.59 and 31.90 %, respectively. A comparative study between strain NEAU-LZS-5(T) and the type strains of closest related species of the genus Streptomyces revealed that it differed from them in morphological, physiological and biochemical characteristics. Therefore, strain NEAU-LZS-5(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces zhaozhouensis sp. nov. is proposed. The type strain is NEAU-LZS-5(T) ( = CGMCC 4.7095(T) = DSM 42101(T)).

Nonomuraea fuscirosea sp. nov., an actinomycete isolated from the rhizosphere soil of rehmannia (Rehmannia glutinosa Libosch).

A novel actinomycete, designated strain NEAU-dht8(T), was isolated from the rhizosphere soil of rehmannia (Rehmannia glutinosa Libosch) and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Nonomuraea. The G+C content of the DNA was 68.47 mol%. On the basis of 16S rRNA gene sequence similarity studies, strain NEAU-dht8(T) was most closely related to Nonomuraea maheshkhaliensis 16-5-14(T) (99.31%), Nonomuraea kuesteri GW 14-1925(T) (98.77%), Nonomuraea coxensis JCM 13931(T) (98.71%), Nonomuraea wenchangensis 210417(T) (98.44 %), Nonomuraea bangladeshensis 5-10-10(T) (98.36%) and Nonomuraea salmonea DSM 43678(T) (98.0%); similarities to other species of the genus Nonomuraea were lower than 98%. Two tree-making algorithms based on 16S rRNA gene sequences showed that the isolate formed a phyletic line with its closest neighbour N. maheshkhaliensis 16-5-14(T). However, the low level of DNA-DNA relatedness allowed the novel isolate to be differentiated from N. maheshkhaliensis 16-5-14(T). Strain NEAU-dht8(T) could also be differentiated from other species of the genus Nonomuraea showing high 16S rRNA gene sequence similarity (98-98.77%) by morphological and physiological characteristics. Thus, strain NEAU-dht8(T) is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea fuscirosea sp. nov. is proposed. The type strain is NEAU-dht8(T) ( = CGMCC 4.7104(T) = DSM 45880(T)).

Streptomyces daqingensis sp. nov., isolated from saline–alkaline soil

A novel strain of actinobacteria, designated strain NEAU-ZJC8T, was isolated from a saline-alkaline soil collected from Heilongjiang Province, north-east China and characterized using a polyphasic approach. Strain NEAU-ZJC8T exhibited morphological, cultural and chemotaxonomic features consistent with its classification as representing a member of the genus Streptomyces. Growth occurred at 16-35 °C, pH 5.0-11.0 and in the presence of 0-11 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid and glycine. Whole-cell hydrolysates mainly contained glucose, galactose and ribose. Predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0. The G+C content of the DNA was 72.7 mol%. A phylogenetic tree based on 16S rRNA sequences showed that strain NEAU-ZJC8T formed a distinct clade within the genus Streptomyces and was closely related to Streptomyces haliclonae DSM 41970T (98.56 % similarity) and Streptomyces marinus NBRC 105047T (97.96 % similarity). A combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-ZJC8T could be distinguished from its closest phylogenetic relatives. Therefore, strain NEAU-ZJC8T represents a novel species of the genus Streptomyces, for which the name Streptomyces daqingensis sp. nov. is proposed. The type strain is NEAU-ZJC8T ( = CGMCC 4.7178T = JCM 30057T).

Saccharothrix carnea sp. nov., an actinobacterium isolated from soil.

A novel actinobacterium, designated strain NEAU-yn17(T), was isolated from a soil sample collected at the wastewater discharge site of a pesticide factory in Harbin, northern China, and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-yn17(T) were consistent with the description of the genus Saccharothrix, such as the spore arrangement, the diamino acid of the peptidoglycan, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-yn17(T) should also be classified in the genus Saccharothrix, with Saccharothrix saharensis DSM 45456(T) (99.52 % sequence similarity) and Saccharothrix xinjiangensis JCM 12329(T) (99.04 %) as the nearest phylogenetic relatives. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-yn17(T) can be distinguished from its closest relatives. Therefore, strain NEAU-yn17(T) represents a novel species of the genus Saccharothrix, for which the name Saccharothrix carnea sp. nov. is proposed. The type strain is NEAU-yn17(T) ( = CGMCC 4.7097(T) = DSM 45878(T)).

Actinoplanes rhizophilus sp. nov., an actinomycete isolated from the rhizosphere of Sansevieria trifasciata Prain

A novel actinomycete, designated strain NEAU-A-2T, was isolated from the rhizosphere soil of Sansevieria trifasciata Prain collected from Heilongjiang province, north-east China. The taxonomic status of this organism was established using a polyphasic approach. The isolate formed irregular sporangia containing motile spores on the substrate mycelium. The whole-cell sugars were xylose and galactose. The predominant menaquinones were MK-9(H10), MK-9(H2), MK-10(H2) and MK-10(H4). The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, three unidentified phospholipids and an unidentified glycolipid. 16S rRNA gene sequence similarity studies showed that strain NEAU-A-2T belongs to the genus Actinoplanes with the highest sequence similarities to Actinoplanes globisporus NBRC 13912T (97.7 % 16S rRNA gene sequence similarity), Actinoplanes ferrugineus IMSNU 22125T (97.5 %), Actinoplanes toevensis MN07-A0368T (97.2 %) and Actinoplanes rishiriensis NBRC 108556T (97.2 %); similarities to type strains of other species of this genus were < 97 %. Two tree-making algorithms showed that strain NEAU-A-2T formed a distinct clade with A. globisporus NBRC 13912T and A. rishiriensis NBRC 108556T. However, low DNA-DNA relatedness values allowed the isolate to be differentiated from the above-mentioned two species of the genus Actinoplanes. Moreover, strain NEAU-A-2T could also be distinguished from the most closely related species by morphological and physiological characteristics. Therefore, in conclusion, isolate NEAU-A-2T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes rhizophilus sp. nov. is proposed. The type strain is NEAU-A-2T ( = CGMCC 4.7133T = DSM 46672T).

Complete genome sequence of Streptomyces cyaneogriseus ssp. noncyanogenus, the thermotolerant producer of commercial antibiotics nemadectin

Streptomyces cyaneogriseus ssp. noncyanogenus is thermotolerant bacterium producing commercially important nemadectin, a kind of macrolide antibiotics, which has been widely used as a biopesticide. Here, we report the complete genome sequence of S. cyaneogriseus ssp. noncyanogenus, which consists of one chromosome (7,762,396bp) with no plasmid. Genome sequence information contributes to understanding the biosynthesis of nemadectin better and provides the basis for analysis of its thermotolerance and biosynthetical potential.

Actinomycetospora rhizophila sp. nov., an actinomycete isolated from rhizosphere soil of a peace lily (Spathi phyllum Kochii).

A novel actinomycete, designated strain NEAU-B-8(T), was isolated from the rhizosphere soil of a peace lily (Spathi phyllum Kochii) collected from Heilongjiang province, north-east China. Key morphological and physiological characteristics as well as chemotaxonomic features of strain NEAU-B-8(T) were congruent with the description of the genus Actinomycetospora , such as the major fatty acids, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. The 16S rRNA gene sequence analysis revealed that strain NEAU-B-8(T) shared the highest sequence similarities with Actinomycetospora lutea JCM 17982(T) (99.3% 16S rRNA gene sequence similarity), Actinomycetospora chlora TT07I-57(T) (98.4 %), Actinomycetospora straminea IY07-55(T) (98.3%) and Actinomycetospora chibensis TT04-21(T) (98.2%); similarities to type strains of other species of this genus were lower than 98%. The phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-B-8(T) formed a distinct branch with A. lutea JCM 17982(T) that was supported by a high bootstrap value of 97% in the neighbour-joining tree and was also recovered with the maximum-likelihood algorithm. However, the DNA-DNA relatedness between strain NEAU-B-8(T) and A. lutea JCM 17982(T) was found to be 50.6 ± 1.2%. Meanwhile, strain NEAU-B-8(T) differs from other most closely related strains in phenotypic properties, such as maximum NaCl tolerance, hydrolysis of aesculin and decomposition of urea. On the basis of the morphological, physiological, chemotaxonomic, phylogenetic and DNA-DNA hybridization data, we conclude that strain NEAU-B-8(T) represents a novel species of the genus Actinomycetospora , named Actinomycetospora rhizophila sp. nov. The type strain is NEAU-B-8(T). ( = CGMCC 4.7134(T) =DSM 46673(T)).

SbbR/SbbA, an Important ArpA/AfsA-Like System, Regulates Milbemycin Production in Streptomyces bingchenggensis

Milbemycins, a group of 16-membered macrolide antibiotics, are used widely as insecticides and anthelmintics. Previously, a limited understanding of the transcriptional regulation of milbemycin biosynthesis has hampered efforts to enhance antibiotic production by engineering of regulatory genes. Here, a novel ArpA/AfsA-type system, SbbR/SbbA (SBI_08928/SBI_08929), has been identified to be involved in regulating milbemycin biosynthesis in the industrial strain S. bingchenggensis BC04. Inactivation of sbbR in BC04 resulted in markedly decreased production of milbemycin, while deletion of sbbA enhanced milbemycin production. Electrophoresis mobility shift assays (EMSAs) and DNase I footprinting studies showed that SbbR has a specific DNA-binding activity for the promoters of milR (the cluster-situated activator gene for milbemycin production) and the bidirectionally organized genes sbbR and sbbA. Transcriptional analysis suggested that SbbR directly activates the transcription of milR, while represses its own transcription and that of sbbA. Moreover, 11 novel targets of SbbR were additionally found, including seven regulatory genes located in secondary metabolite biosynthetic gene clusters (e.g., sbi_08420, sbi_08432, sbi_09158, sbi_00827, sbi_01376, sbi_09325, and sig24sbh) and four well-known global regulatory genes (e.g., glnRsbh, wblAsbh, atrAsbh, and mtrA/Bsbh). These data suggest that SbbR is not only a direct activator of milbemycin production, but also a pleiotropic regulator that controls the expression of other cluster-situated regulatory genes and global regulatory genes. Overall, this study reveals the upper-layer regulatory system that controls milbemycin biosynthesis, which will not only expand our understanding of the complex regulation in milbemycin biosynthesis, but also provide a basis for an approach to improve milbemycin production via genetic manipulation of SbbR/SbbA system.

Bacillus solisilvae sp. nov., isolated from forest soil

A novel Gram-stain-positive, motile, endospore-forming, rod-shaped bacterial strain, NEAU-cbsb5T, was isolated from forest soil from Changbai Mountain, Heilongjiang Province, China. The isolate grew at 15-40 °C (optimum 30 °C), at pH 6.0-8.0 (optimum pH 7.0) and in the presence of up to 4 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NEAU-cbsb5T formed a distinct lineage within the genus Bacillus and was most closely related to Bacillus acidiceler DSM 18954T (99.1 % similarity) and Bacillus luciferensis JCM 12212T (99.0 %). 16S rRNA gene sequence similarity to sequences of the type strains of other Bacillus species was less than 96.0 %. Average nucleotide identity (ANI) values between NEAU-cbsb5T and its most closely related species were 78.72-84.75 % by ANIm, ANIb and OrthoANIu analysis. The in silico DNA-DNA hybridization values between strain NEAU-cbsb5T and its close relatives B. acidiceler DSM 18954T and B. luciferensis JCM 12212T were both 23.80 %, again indicating they belong to different taxa. The major cellular fatty acids of NEAU-cbsb5T were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the predominant menaquinones were MK-7 and MK-6. The genomic DNA G+C content was 33.0 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain NEAU-cbsb5T was classified as a representative of a novel species in the genus Bacillus, for which the name Bacillus solisilvae sp. nov. is proposed. The type strain is NEAU-cbsb5T (=CGMCC 1.14993T=DSM 100485T).