Ll-diaminopimelic Acid Research Articles

Streptomyces yaizuensis sp. nov., a berninamycin C-producing actinomycete isolated from sponge.

While screening for antibiotics in a marine sample, we discovered a berninamycin C-producing actinomycete, designated YSPA8T, isolated from a sponge. A polyphasic approach was used to determine the taxonomic position of the strain. Strain YSPA8T formed sympodially branched aerial mycelia that ultimately segment into chains of spores. Comparative and phylogenetic analyses of the 16S rRNA gene sequence showed that strain YSPA8T were closely related to Streptomyces clavuligerus ATCC 27064T (99.66%), Streptomyces amakusaensis NRRL B-3351T (98.69%), Streptomyces inusitatus NBRC 13601T (98.48%), and 'Streptomyces jumonjinensis' JCM 4947 (98.41%). The phylogenetic tree using the 16S rRNA gene sequences, and both phylogenomic trees suggested that the closest relative of strain YSPA8T was S. clavuligerus ATCC 27064T. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain YSPA8T and S. clavuligerus ATCC 27064T were 84.1%, 28.9%, and 82.5%, respectively, which were below the thresholds of 95%, 70%, and 95% for a prokaryotic conspecific assignment. The G + C of the strain YSPA8T was 72.6%. Whole-cell hydrolysates of strain YSPA8T contained LL-diaminopimelic acid. The predominant menaquinones were MK-9(H6) (49%) and MK-9(H8) (48%), and the major fatty acids were C16:0 (26.8%), C16:1 ω7c/ω6c (17.2%), iso-C16:0 (16.0%), and iso-C15:0 (12.5%). The major phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, and other unidentified phospholipids. Based on the phenotypic, phylogenetic, genomic, and chemotaxonomic data, strain YSPA8T represents a novel species of the genus Streptomyces, and the proposed name for this species is Streptomyces yaizuensis sp. nov. The type strain is YSPA8T (=NBRC 115866T = TBRC 17196T).

Description of Streptomyces siderophoricus sp. nov., a promising nocardamine-producing species isolated from the rhizosphere soil of Mangifera indica.

An actinomycete, designated strain CH9-7T, was isolated from the rhizosphere soil of Mangifera indica. The morphological and chemotaxonomic properties, such as the production of spiral spore chains and the presence of LL-diaminopimelic acid in the peptidoglycan, showed that it belongs to the genus Streptomyces. Based on the 16S rRNA gene analysis, it was confirmed that strain CH9-7T was a member of the genus Streptomyces and revealed 99.9% 16S rRNA gene sequence similarity to its closest relative strains, Streptomyces lydicus NBRC 13058 T and Streptomyces chattanoogensis NBRC 12754 T. Although the strain showed high 16S rRNA gene sequence similarity values, however, genome relatedness indexes exhibited that the average nucleotide identity based on the MUMmer (ANIm) algorithm, the average amino acid identity (AAI), and the digital DNA-DNA hybridization values between strain CH9-7T and its closest phylogenomic relatives were below the threshold values for delineation of a novel species, (ANIm ranging from 87.5 to 88.6, AAI ranging from 80.6 to 84.6, and dDDH ranging from 28.4 to 31.7), respectively. A taxonomic position of strain CH9-7T in the phylogenomic tree showed that the closest relative strain was S. lydicus NBRC 13058 T. The comparative phenotypic studies between strain CH9-7T and its closest relatives revealed that strain CH9-7T could be classified as a novel species of the genus Streptomyces. Thus, the name Streptomyces siderophoricus sp. nov. is proposed for the strain. The type strain is CH9-7T ( = TBRC 17833 T = NBRC 116426 T). The chemical investigation led to the isolation of four known compounds (compounds 1-4). Among these compounds, compound 1 was identified to be nocardamine, a promising bioactive substance.

Streptomyces beigongshangae sp. nov., isolated from baijiu fermented grains, could transform ginsenosides of Panax notoginseng.

A Gram-stain-positive actinomycete, designated REN17T, was isolated from fermented grains of Baijiu collected from Sichuan, PR China. It exhibited branched substrate mycelia and a sparse aerial mycelium. The optimal growth conditions for REN17T were determined to be 28 °C and pH 7, with a NaCl concentration of 0 % (w/v). ll-Diaminopimelic acid was the diagnostic amino acid of the cell-wall peptidoglycan and the polar lipids were composed of phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid, two unidentified lipids and four unidentified glycolipids. The predominant menaquinone was MK-9 (H2), MK-9 (H4), MK-9 (H6) and MK-9 (H8). The major fatty acids were iso-C16 : 0. The 16S rRNA sequence of REN17T was most closely related to those of Streptomyces apricus SUN 51T (99.8 %), Streptomyces liliiviolaceus BH-SS-21T (99.6 %) and Streptomyces umbirnus JCM 4521T (98.9 %). The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identify values between REN17T and its closest replated strain, of S. apricus SUN 51T, were 35.9, 88.9 and 87.3 %, respectively. Therefore, REN17T represents a novel species within the genus Streptomyces, for which the name Streptomyces beigongshangae sp. nov. is proposed. The type strain is REN17T (=GDMCC 4.193T=JCM 34712T). While exploring the function of the strain, REN17T was found to possess the ability to transform major ginsenosides of Panax notoginseng (Burk.) F.H. Chen (Araliaceae) into minor ginsenoside through HPLC separation, which was due to the presence of β-glucosidase. The recombinant β-glucosidase was constructed and purified, which could produce minor ginsenosides of Rg3 and C-K. Finally, the enzymatic properties were characterized.

Streptomyces herbicida sp. nov., a novel actinomycete with antibacterial and herbicidal activity isolated from soil.

A novel actinobacterial strain (NEAU-HV9T) showing antibacterial activity against Ralstonia solanacearum and herbicidal activity against Amaranthus retroflexus L. was isolated from soil sampled in Bama yao Autonomous County, Hechi City, Guangxi Zhuang Autonomous Region. The strain is aerobic and Gram-positive. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-HV9T belonged to the genus Streptomyces and showed high 16S rRNA sequence similarity to Streptomyces panaciradicis 1MR-8T (98.90 %), Streptomyces sasae JR-39T (98.89 %) and Streptomyces barringtoniae JA03T (98.69 %) and less than 98.5 % similarity to other members of the genus Streptomyces. The cell wall of strain NEAU-HV9T contained ll-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose and ribose. The predominant menaquinones were composed of MK-9(H2) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The major fatty acids were C16 : 0, iso-C16 : 0 and C17 : 1 ω8c. The genomic DNA G+C content of strain NEAU-HV9T was 70.6 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA-DNA hybridization results and some phenotypic characteristics. Meanwhile, strain NEAU-HV9T displayed herbicidal activity. Therefore, strain NEAU-HV9T represents a novel species within the genus Streptomyces, for which the name Streptomyces herbicida sp. nov. is proposed, with strain NEAU-HV9T (=CCTCC AA 2019088T=DSM 113364T) as the type strain.

Nocardioides limicola sp. nov., an alkaliphilic alkane degrading bacterium isolated from oilfield alkali-saline soil.

A Gram-stain-positive, rod-shaped, non-spore-forming, alkane degrading bacterium, designated DJM-14T, was isolated from oilfield alkali-saline soil in Heilongjiang, Northeast China. On the basis of 16S rRNA gene sequencing, strain DJM-14T was shown to belong to the genus Nocardioides, and related most closely to Nocardioides terrigena KCTC 19,217T (95.53% 16S rRNA gene sequence similarity). Strain DJM-14T was observed to grow at 25-35°C, pH 7.0-11.0, in the presence of 0-6.0% (w/v) NaCl. The predominant respiratory quinone was MK-8 (H4) and LL-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major fatty acids were identified as iso-C16:0 and C18:1 ω9c. It contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The genome (3,722,608bp), composed of 24 contigs, had a G + C content of 69.6mol%. Out of the 3667 predicted genes, 3618 were protein-coding genes, and 49 were ncRNAs. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of strain DJM-14T against genomes of the type strains of related species in the same family ranged between 18.7% and 20.0%; 68.8% and 73.6%, respectively. According to phenotypic, genotypic and phylogenetic data, strain DJM-14T represents a novel species in the genus Nocardioides, for which the name Nocardioides limicola sp. nov. is proposed and the type strain is DJM-14T (= CGMCC 4.7593T, =JCM 33,692T). In addition, novel strains were able to grow with n-alkane (C24-C36) as the sole carbon source. Multiple copies of alkane 1-monooxygenase (alkB) gene, as well as alcohol dehydrogenase gene and aldehyde dehydrogenase gene involved in the alkane assimilation were annotated in the genome of type strain DJM-14T.

Streptomyces changanensis sp. nov. Isolated from Soil in China.

An aerobic, Gram-positive, and non-motile actinomycete, designated HL-66T, was isolated from a soil sample collected in the Meridian Valley, Shaanxi Province, China. Morphological, chemotaxonomic, and phylogenetic characteristics showed a high similarity to the genus Streptomyces. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbour of HL-66T were Streptomyces lavendofoliae NBRC 12882T (99.17%), Streptomyces gobitricini NBRC 15419T (99.03%) and Streptomyces roseolilacinus NBRC 12815T (98.96%). Genome relatedness indexes revealed that the average nucleotide identity and digital DNA-DNA hybridization values between HL-66T and its closest phylogenomic relative (S. roseolilacinus JCM 4335T) were 88.61% and 32.10%, respectively. The cell-wall peptidoglycan contains LL-diaminopimelic acid. Predominant menaquinones are MK-9 (H6), MK-9(H4) and MK-9(H8). The major cellular fatty acids were iso-C16:0, anteiso-C15:0, iso-C16:1 H, and C16:1 ω7c. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, and an unknown phospholipid. Based on phylogenetic analyses, genome-genome distance calculation, and average nucleotide identity, strain HL-66T represents a novel species of the genus Streptomyces. Therefore, a new species Streptomyces changanensis sp. nov. is proposed with strain HL-66T (= CGMCC 22674 = JCM 35800) as the type strain.

Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment.

Three Gram-stain-positive, non-motile, short rod-shaped, catalase-positive and oxidase-negative actinomycete strains (SOB44T, SOB72T and SOB77T) were isolated from a deep-sea sediment sample collected from the Western Pacific Ocean. Cells of the three strains showed optimum growth at 30 °C and pH 7.0. Strains SOB44T, SOB72T and SOB77T could tolerate up to 10, 9 and 9 % (w/v) NaCl concentration and grow at pH 5.0-12.0, 5.0-11.0 and 5.0-11.0, respectively. Phylogenetic results based on 16S rRNA gene sequences showed that the three isolates belonged to the genus Nocardioides and were identified as representing three novel species based on 78.0-93.1 % average nucleotide identity and 21.3-50.0 % DNA-DNA hybridization values with closely related reference strains. Strains SOB44T, SOB72T and SOB77T showed highest 16S rRNA gene sequence similarity to Nocardioides salarius CL-Z59T (99.2 %), Nocardioides deserti SC8A-24T (99.2 %) and Nocardioides marmotae zg-579T (98.5 %), respectively. All three strains had MK-8(H4) as the respiratory quinone, iso-C16 : 0 as the major fatty acid, and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the major polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan of all three isolates was ll-diaminopimelic acid. The DNA G+C contents of strains SOB44T, SOB72T and SOB77T were 71.1, 72.9 and 72.9 mol%, respectively. Based on the phenotypic, phylogenetic and genotypic data, strains SOB44T, SOB72T and SOB77T clearly represent three novel taxa within the genus Nocardioides, for which the names Nocardioides cremeus sp. nov. (type strain SOB44T=JCM 35774T= MCCC M28400T), Nocardioides abyssi sp. nov. (type strain SOB72T=JCM 35775T=MCCC M28318T) and Nocardioides oceani sp. nov. (type strain SOB77T=JCM 35776T=MCCC M28544T) are proposed.

Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks.

A novel Streptomyces strain, designated 3_2T, was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2T can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2T was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2T, compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2T to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2T possessed MK-9 (H6) and MK-9 (H8) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C16:0 (23.6%) and anteiso-C15:0 (10.4%). The fermentation products of strain 3_2T were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2T was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2T can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2T (= JCM 34935T = GDMCC 4.217T).

Streptomyces silvisoli sp. nov., a polyene producer, and Streptomyces tropicalis sp. nov., two novel actinobacterial species from peat swamp forests in Thailand.

Two novel actinobacterial strains, designated RB6PN23T and K1PA1T, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing ll-diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23T was most closely related to Streptomyces rubrisoli (99.1 % sequence similarity) and Streptomyces ferralitis (98.5%), while strain K1PA1T showed 98.8 and 98.7% sequence similarities to Streptomyces coacervatus and Streptomyces griseoruber, respectively. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % ANI and 70 % dDDH). The genomes of strains RB6PN23T and K1PA1T were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23T and K1PA1T encode 37 and 24 putative biosynthetic gene clusters, respectively, and in silico analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23T and K1PA1T represented two novel species in the genus Streptomyces. The names proposed for these strains are Streptomyces silvisoli sp. nov. (type strain RB6PN23T=TBRC 17040T=NBRC 116113T) and Streptomyces tropicalis sp. nov. (type strain K1PA1T=TBRC 17041T=NBRC 116114T). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23T, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23T exhibited strong antifungal activity against Fusarium verticillioides, Fusarium fujikuroi and Bipolaris zeicola. This finding suggests that strain RB6PN23T could be a promising candidate for biological control of fungal diseases.

Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand.

A novel Gram-stain-positive, aerobic actinobacterial strain, designated GXMU-J15T, was isolated from dry mudflat sand. A polyphasic approach was employed for its taxonomic characterization. The strain developed extensively branched yellowish white to light yellow substrate mycelia and white aerial mycelia, and produced smooth cylindrical spores in a loose straight spore chain on International Streptomyces Project 2-7 agar media. Strain GXMU-J15T grew at 20-50 °C (optimum, 35 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl. Analysis of 16S rRNA gene sequences indicated that strain GXMU-J15T represents a member of the genus Streptomyces. Strain GXMU-J15T showed the highest 16S rRNA gene sequence similarity to Streptomyces lusitanus CGMCC 4.1745T (99.1 %) and Streptomyces thermocarboxydus CGMCC 4.1883T (98.8 %). Phylogenetic tree analysis based on multilocus sequence analysis (MLSA) and whole genome sequence construction revealed that strain GXMU-J15T was most closely related to Streptomyces cupreus PSKA01T, Streptomyces cinnabarinus DSM 40467T and Streptomyces davaonensis JCM 4913T. The MLSA and genome-to-genome distances between strain GXMU-J15T and its relatives were 0.0418, 0.0443 and 0.0485 and 0.1237, 0.1188 and 0.1179, respectively. The results of orthologous average nucleotide identity and digital DNA-DNA hybridization analysis corroborated the results of the MLSA and whole genome sequence evolution analysis, indicating that the novel isolate represents a distinct species of the genus Streptomyces. The whole-cell sugars of strain GXMU-J15T were xylose, glucose and galactose. The characteristic diamino acid in the cell-wall hydrolysate was ll-diaminopimelic acid. The lipids contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylglycerides, phosphatidylcholine, two phospholipids of an unknown structure containing glucosamine, one unknown phospholipid and two unknown lipids. The major cellular fatty acid components were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main respiratory quinone types were MK-9(H6) and MK-9(H8). The whole genome size of strain GXMU-J15T was 8.68 Mbp, with 71.23 mol% G+C content. Genomic analysis indicated that strain GXMU-J15T has the potential to synthesize polyketides, terpenes and a series of important antibiotics besides the gene cluster for melanin synthesis. Based on these genotypic and phenotypic data, strain GXMU-J15T is proposed to represent a new species of the genus Streptomyces named Streptomyces fuscus sp. nov. The type strain is GXMU-J15T (=MCCC 1K08211T=JCM 35917T).

Nocardioides pini sp. nov. and Nocardioides pinisoli sp. nov., two novel actinomycetes isolated from Pinus densiflora.

Two novel Gram-positive bacteria designated as strains STR2T and STR3T were isolated from the rhizosphere of a Pinus densiflora sample collected from Goyang-si, Republic of Korea. Strains STR2T and STR3T were aerobic, rod shaped, non-sporulated, catalase negative, oxidase negative and non-motile bacteria. They grew at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-2% NaCl (optimum, 0 %, w/v). The chemotaxonomic and morphological characteristics of the novel strains were consistent with those of the members of Nocardioides. The phylogenetic analysis of the 16S rRNA gene sequences revealed that STR2T was closely related to N. cavernae YIM A1136T (99.3 %) and N. flavus Y4T (99.1 %), and STR3T was closely related to N. exalbidus DSM 22017T (99.0 %), N. baculatus G10T (98.8 %) and N. hwasunensis HFW-21T (98.7 %). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values of STR2T and STR3T with the most closely related strains that have publicly available whole genomes were 83.1-89.8 %, 80.9-89.6% and 26.2-39.1 %, respectively. The cell-wall peptidoglycan of strain STR2T and STR3T contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids in STR2T and STR3T were iso-C16 : 0 and C17 : 1 ω8c, and the predominant quinone was MK-8(H4). Their polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and other polar lipids. The draft genome sequences showed that the genomic DNA G+C content of STR2T and STR3T were both 72.2 mol%. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that STR2T and STR3T could represent novel Nocardioides species. Their proposed names were as follows: Nocardioides pini sp. nov. for strain STR2T (=KACC 22784T=TBRC 16336T) and Nocardioides pinisoli sp. nov. for strain STR3T (= KACC 22785T=TBRC 16337T).

Streptomyces learnhanii sp. nov., unveiling a Mangrove-Derived Novel “Modern Actinobacteria” in Malaysia

Streptomyces learnhanii sp. nov. MUM 203JT was isolated from Malaysia mangrove soil. This Gram-positive bacterium produces pale greenish-yellow aerial and greyish-yellow substrate mycelia on ISP 2 agar. The taxonomy status of strain MUM 203JT was determined via a polyphasic approach comprising phenotypic observations, genomic and phylogenetic analyses, and chemotaxonomic analyses. The strain demonstrated typical Streptomyces features based on a series of phenotypic and chemotaxonomic evaluations. In particular, the cell wall peptidoglycan contained LL-diaminopimelic acid, and the predominant menaquinones detected include MK9(H8). Analysis of whole-cell sugars revealed the presence of glucose, ribose and mannose. The polar lipid profile of the strain comprised lipid, glycolipid, phospholipid, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, phosphoglycolipid, and diphosphatidylglycerol. The major cellular fatty acids (>10.0 %) were anteiso-C15:0 (24.7 %), anteiso-C17:0 (16.4 %), iso-C16:0 (15.7 %), iso-C15:0 (11.5 %), and C16:0 (11.1 %). The closely related type strains for strain MUM 203JT, as determined by phylogenetic analysis, include Streptomyces coeruleorubidus JCM 4359T (98.8 %), Streptomyces coeruleoprunus JCM 6919T (98.5 %), Streptomyces thermocarboxydovorans NBRC 16324T (98.1 %). The DNA–DNA relatedness values between strain MUM 203JT and closely related type strains ranged from 10.7 ± 0.6 % to 23.3 ± 4.7 %. Strain MUM 203JT has a genome size of 6,446,886 bp, with DNA G + C content of 72.26 mol%. Based on the polyphasic study of strain MUM 203JT, it can be concluded that this strain represents a novel species, for which the name Streptomyces learnhanii sp. nov. is proposed. The type strain is MUM 203JT (= NBRC 114250T = MCCC 1K04200T).

Genome-based classification of Streptomyces anatolicus sp. nov., an actinobacterium with antimicrobial and cytotoxic activities, and reclassification of Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis.

During the course of isolating novel actinobacteria producing bioactive metabolites, strain BG9HT was obtained from an arid soil sample in Erzurum, Turkey. Pairwise sequence comparisons for 16S rRNA gene sequences showed the strain was a member of the genus Streptomyces and it shared the highest 16S rRNA gene sequence identity of 99.7% with Streptomyces huasconensis HST28T. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity revealed that strain BG9HT represents a novel species within the genus Streptomyces. The polyphasic analysis also confirmed that the strain has typical characteristics of the genus Streptomyces. The strain has LL-diaminopimelic acid as diagnostic amino acid, and galactose, mannose and trace amounts of glucose and ribose as whole-cell sugars. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unidentified aminolipids, phospholipids and lipids. Major isoprenoid quinones were MK-9(H6), MK-9(H4), and MK-9(H8). Its genome size is approximately 7.2Mb with 71.2% G+C content. The methanolic extract of strain BG9HT showed antimicrobial and cytotoxic activities. Further genomic analyses of strain BG9HT confirmed its high potential to produce novel secondary metabolites. On the basis of phenotypic and phylogenetic analyses, strain BG9HT represents a novel species of the genus Streptomyces, for which Streptomyces anatolicus sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to the biopharmaceutical industry. We also propose Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis as a result obtained through analysis of overall genome relatedness indices.

Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis.

Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae. They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis, S. parmotrematis and S. rubrisoli; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis, S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.

Streptomyces zingiberis sp. nov., an endophytic actinobacterium isolated from the root tissue of Zingiber montanum.

An endophytic actinobacterium, designated strain PLAI 1-29T, was isolated from the root tissue of Zingiber montanum collected from Pathum Thani province, Thailand. Strain PLAI 1-29T was characterized using a polyphasic taxonomic approach. It typically exhibited morphological and chemotaxonomic properties of the genus Streptomyces. Strain PLAI 1-29T produced a spiral spore chain on aerial mycelium and grew at 15-40 °C, pH 6-10 on International Streptomyces Project 2 agar. The maximum NaCl concentration for growth was 9 % (w/v). Cells of strain PLAI 1-29T presented ll-diaminopimelic acid, arabinose, galactose and ribose. The detected phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The genome-based taxonomic details revealed the assignment of strain PLAI 1-29T to the genus Streptomyces and exhibited low threshold values for the delineation of a novel species by average nucleotide identity-blast (84.0%), average amino acid identity (80.0%) and digital DNA-DNA hybridization (27.6%) with its closest type strain, Streptomyces xinghaiensis S187T. Furthermore, several differential physiological and biochemical characteristics were detected between strain PLAI 1-29T and the closest type strain. Based on the combined phenotypic and genomic features, strain PLAI 1-29T (=TBRC 7645T=NBRC 113170T) is considered to represent a new Streptomyces species, for which we propose the name Streptomyces zingiberis sp. nov.

Streptomyces cylindrosporus sp. nov. and Streptomyces spinosisporus sp. nov.: two new endophytic actinobacteria isolated from the roots of Barleria lupulina Lindl.

Two endophytic actinobacteria, designated as strains 7R015T and 7R016T, were isolated from the roots of Barleria lupulina collected in Thailand. The morphological characteristics and results of chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains represented members of the genus Streptomyces. They contained ll-diaminopimelic acid in the peptidoglycan. Ribose and glucose were detected as the whole-cell sugars. MK-9(H4), MK-9(H6) and MK-9(H8), were found as the membrane menaquinone. The predominant cellular fatty acids detected were iso-C16 : 0 and anteiso-C15 : 0. The genomes of both strains harboured biosynthetic gene clusters for melanin, terpene, lanthipeptide, polyketides, non-ribosomal peptide synthetase, siderophore and ectoine. The 16S rRNA gene sequence of 7R015T showed the highest similarity to that of Streptomyces pseudovenezuelae DSM 40212T (98.6 %), Streptomyces cyaneus NRRL B2296T (98.6 %) and Streptomyces curacoi DSM 40107T (98.6 %). Strain 7R016T showed the highest 16S rRNA gene sequence similarity to Streptomyces gilvifuscus NBRC 110904T (98.2 %), which is lower than the threshold value for 16S rRNA gene sequence similarity for differentiation at the species level (98.65 %). Comparative genome analysis revealed that the genomes of 7R015T, 7R016T and the closely related type strains had an average nucleotide identity (ANI) of less than 95 % and a digital DNA-DNA hybridisation (dDDH) of less than 70 %, the thresholds for species demarcation. On the basis of the results of the polyphasic study, strains 7R015T and 7R016T represent novel species of the genus Streptomyces and are named herein as Streptomyces cylindrosporus sp. nov. (=NBRC 115200T = TBRC 14542T) for strain 7R015T and Streptomyces spinosisporus sp. nov. (=NBRC 115201T = TBRC 14543T) for strain 7R016T.

Yinghuangia soli sp. nov., isolated from soil of weathering dolomite in a karst area.

A Gram-stain-positive, aerobic actinomycete strain, designated KLBMP 8922T, was isolated from a soil sample collected from weathering dolomite crust in Guizhou Province, PR China. KLBMP 8922T showed the 16S rRNA gene similarities to Yinghuangia seranimata CCTCC AA 206006T (98.7 %), Yinghuangia catbensis VN07A0015T (98.3 %) and Yinghuangia aomiensis M24DS4T (98.2 %). The taxonomic status of this strain was investigated by using a polyphasic approach. The aerial mycelia of KLBMP 8922T formed spore chains, and spores were cylindrical with smooth surfaces. The whole-cell sugars were ribose, mannose and galactose with traces of glucose and xylose. The diagnostic amino acids of the cell wall were ll-diaminopimelic acid, alanine and glutamic acid. The predominant menaquinones were MK-9(H6) and MK-9(H8). The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and iso-C16 : 1H. The genomic DNA G+C content was 72.0 mol%. The digital DNA-DNA hybridization (dDDH) value between KLBMP 8922T and Y. seranimata CCTCC AA 206006T was 24.1 %, and the average nucleotide identity (ANI) value was 81.0 %. On the basis of a combination of morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 8922T represents a novel species of the genus Yinghuangia for which the name Yinghuangia soli sp. nov. is proposed. The type strain was KLBMP 8922T (= CGMCC 1.19360T = NBRC 115572T).

Identification of Nocardioides marmotae sp. nov. and Nocardioides faecalis sp. nov., two new members of the genus Nocardioides.

A polyphasic taxonomic characterization of two novel strain pairs (designated zg-579T/zg-578 and zg-536T/zg-ZUI104) isolated from the faeces of Marmota himalayana was conducted based on phylogenetic analysis of the nearly full-length 16S rRNA gene and genome, digital DNA-DNA hybridization, ortho-average nucleotide identity (Ortho-ANI), and phenotypic and chemotaxonomic traits. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed that strain zg-579T was most closely related to Nocardioides dokdonensis FR1436T (97.57 %) and Nocardioides deserti SC8A-24T (97.36 %), whereas strain zg-536T had the highest similarity to Nocardioides caeni MN8T (98.33 %), Nocardioides convexus W2-2-3T (98.26 %) and Nocardioides daeguensis 2C1-5T (98.19 %). Low levels of DNA-DNA relatedness and Ortho-ANI values (19.8-31.0 %/78.6-88.2 %, zg-579T; 19.9-31.3 %/78.8-86.2 %, zg-536T) between the two new type strains and previously known species within the genus Nocardioides support the hypothesis that the four newly characterized strains could be considered to represent two novel species within this genus. The dominant cellular fatty acids found in strain pair zg-536T/zg-ZUI104 were iso-C16 : 0 and C18 : 1 ω9c, whereas C17 : 1 ω8c was major component in zg-579T/zg-578. Galactose and ribose were the main cell-wall sugars in these two new strain pairs. Diphosphatidylglycerol (DPG), phosphatidylcholine, phosphatidylglycerol (PG) and phosphatidylinositol (PI) were the major polar lipids in zg-579T, whereas DPG, PG and PI predominated in zg-536T. Both strain pairs had MK8(H4) as the major respiratory quinone and ll-diaminopimelic acid as the major cell-wall peptidoglycan. The optimal growth conditions for the two novel strain pairs were 30 °C, pH 7.0 and 0.5 % NaCl (w/v). Based on these polyphasic characterizations, two novel species within the genus Nocardioides are proposed, i.e. Nocardioides marmotae sp. nov. and Nocardioides faecalis sp. nov., with zg-579T (=CGMCC 4.7663T=JCM 33892T) and zg-536T (=CGMCC 4.7662T=JCM 33891T) as the type strains.

Streptomyces salinarius sp. nov., an actinomycete isolated from solar saltern soil.

An actinobacterium, designated strain SS06011T, was isolated from solar saltern soil collected from Samut Sakhon province, Thailand. The taxonomic position of this strain was established using the polyphasic taxonomic approach. The strain produced grey aerial spore mass on International Streptomyces Project 2 seawater agar that differentiated into spiral spore chains with rugose-surfaced spores. Strain SS06011T was found to have ll-diaminopimelic acid in the cell peptidoglycan. Whole-cell hydrolysates contained galactose, glucose and ribose. MK-9(H6) and MK-9(H4) were major menaquinones. The major cellular fatty acids comprised iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were detected in cells. These characteristics were coincident with the typical morphological and chemotaxonomic properties of the genus Streptomyces. The taxonomic affiliation at the genus level of this strain could also be confirmed by its 16S rRNA gene sequence data. Strain SS06011T showed the highest 16S rRNA gene sequence similarity to Streptomyces ardesiacus NRRL B-1773T (99.1 %), Streptomyces coelicoflavus NBRC 15399T (99.1 %) and Streptomyces hyderabadensis OU-40T (99.1 %). Digital DNA-DNA hybridization (dDDH), average nucleotide identity-blast (ANIb) and average amino acid identity (AAI) values between strain SS06011T and its closely related type strains, S. ardesiacus NBRC 15402T, S. coelicoflavus NBRC 15399T and S. hyderabadensis JCM 17657T, were in the range of 45.4-48.4 % (for dDDH), 90.8-91.9 % (for ANIb) and 90.8-91.7 % (for AAI), respectively, which are lower than the cut-off criteria for species delineation. The DNA G+C content of genomic DNA was 71.9 mol%. With the differences in physiological, biochemical and genotypic data, strain SS06011T could be discriminated from its closest neighbours. Thus, strain SS06011T should be recognized as representing a novel species of the genus Streptomyces, for which the name Streptomyces salinarius sp. nov. is proposed. The type strain is SS06011T (=TBRC 9951T=NBRC 113998T).

Streptomyces beihaiensis sp. nov., a chitin-degrading actinobacterium, isolated from shrimp pond soil.

A Gram-stain-positive actinobacterium, designated strain GXMU-J5T, was isolated from a sample of shrimp pond soil collected in Tieshangang Saltern, Beihai, PR China. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. The organism formed an extensively branched substrate mycelium, with abundant aerial hyphae that differentiated into spores. Phylogenetic analysis of 16S rRNA gene sequences showed that strain GXMU-J5T was most related to Streptomyces kunmingensis DSM 41681T (similarity 97.74 %) and Streptomyces endophyticus YIM 65594T (similarity 96.80 %). However, the values of digital DNA-DNA hybridization, average nucleotide identity and evolutionary distance of multilocus sequence analysis between strain GXMU-J5T and its closest relatives indicated that it represented a distinct species. Strain GXMU-J5T contained ll-diaminopimelic acid and the major whole-cell hydrolysates were xylose and galactose. The predominant menaquinones of strain GXMU-J5T were revealed as MK-9(H4), MK-9(H6) and MK-9(H8). The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole genome size of strain GXMU-J5T was 6.79 Mbp with a 71.39 mol% G+C content. Genomic analysis indicated that strain GXMU-J5T had the potential to degrade chitin. On the basis of these genotypic and phenotypic data, it is supported that strain GXMU-J5T represents a novel species of the genus Streptomyces, for which the name Streptomyces beihaiensis sp. nov. is proposed. The type strain is strain GXMU-J5T (=MCCC 1K08064T=JCM 35629T).