Streptomyces silvae sp. nov., isolated from forest soil.
ABSTRACT: A bacterial strain, named For3T, was isolated from forest soil sampled in Champenoux, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Streptomycetaceae and, more specifically, to the genus Streptomyces. The strain had 99.93% 16S rRNA gene sequence similarity to its closest relative strains Streptomyces pratensis ATCC 33331T, Streptomyces anulatus ATCC 27416T, Streptomyces setonii NRRL ISP-5322T and Kitasatospora papulosa NRRL B-16504T. The phylogenomic tree using the genome blast distance phylogeny method showed that the closest relative strain was Streptomyces atroolivaceus NRRL ISP-5137T and that For3T represents a new branch among the Streptomyces. Genome relatedness indexes revealed that the average nucleotide identity and digital DNA-DNA hybridization values between For3T and its closest phylogenomic relative (S. atroolivaceus NRRL ISP-5137T) were 88.39 and 39.2 %, respectively. The G+C content of the genome was 71.4 mol% and its size was 7.96 Mb with 7492 protein-coding genes. Strain For3T harboured complete metabolic pathways absent in the closest relative strains such as cellulose biosynthesis, glycogen degradation I, glucosylglycerate biosynthesis I. Anteiso-C15:0, iso-C15:0, anteiso-C17:0 and MK-9(H4)/MK-9(H6) were the predominant cellular fatty acids and respiratory quinones, respectively. Phenotypic and genomic data supported the assignment of strain For3T to a novel species Streptomyces silvae sp. nov., within the genus Streptomyces, for which the type strain is For3T (=CIP 111908T=LMG 32186T).
Project description:Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing <i>Streptomyces</i> strain expressing unique genomic and phenotypic characteristics, P38-E01 <sup><i>T</i></sup> , was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01 <sup><i>T</i></sup> was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus <i>Streptomyces</i>, but it was not closely affiliated with other described species. The closest related type strains were <i>Streptomyces daliensis</i> YIM 31724 <sup><i>T</i></sup> (98.6%), <i>Streptomyces rimosus</i> subsp. <i>rimosus</i> ATCC 10970 <sup><i>T</i></sup> (98.4%), and <i>Streptomyces sclerotialus</i> NRRL ISP-5269 <sup><i>T</i></sup> (98.3%). Predominant fatty acids were C<sub>16:0</sub> iso, C<sub>16:0</sub>, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H<sub>6</sub>), MK-10(H<sub>4</sub>), and MK9(H<sub>4</sub>). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01 <sup><i>T</i></sup> was found to inhibit the growth of the pathogenic yeast <i>Candida albicans</i> ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01 <sup><i>T</i></sup> were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01 <sup><i>T</i></sup> from its closest neighbors; thus, this isolate represents a novel species of the genus <i>Streptomyces</i> for which the name <i>Streptomyces tardus</i> sp. nov. (P38-E01 <sup><i>T</i></sup> = CCM 9049 <sup><i>T</i></sup> = DSM 111582 <sup><i>T</i></sup> ) is proposed.
Project description:The taxonomic position of a novel aerobic, Gram-positive actinobacteria, designated strain RB5<sup>T</sup>, was determined using a polyphasic approach. The strain, isolated from the gut of the fungus-farming termite <i>Macrotermes natalensis</i>, showed morphological, physiological and chemotaxonomic properties typical of the genus <i>Streptomyces</i>. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbour of RB5<sup>T</sup> was <i>Streptomyces polyrhachis</i> DSM 42102<sup>T</sup> (98.87 %). DNA-DNA hybridization experiments between strain RB5<sup>T</sup> and <i>S. polyrhachis</i> DSM 42102<sup>T</sup> resulted in a value of 27.4 % (26.8 %). The cell wall of strain RB5<sup>T</sup> contained ll-diaminopimelic acid as the diagnostic amino acid. Mycolic acids and diagnostic sugars in whole-cell hydrolysates were not detected. The strain produced the following major phospholipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannoside and phosphatidylserine. The menaquinone profile showed hexa- and octahydrogenated menaquinones containing nine isoprene units [MK-9(H<sub>6</sub>) and MK-9(H<sub>8</sub>)]. The strain exhibited a fatty acid profile containing the following major fatty acids: 12-methyltridecanoic acid (iso-C<sub>14 : 0</sub>) 12-methyltetradecanoic acid (anteiso-C<sub>15 : 0</sub>), 13-methyltetradecanoic acid (iso-C<sub>15 : 0</sub>) and 14-methylpentadecanoic acid (iso-C<sub>16 : 0</sub>). Here, we propose a novel species of the genus <i>Streptomyces - Streptomyces smaragdinus</i> with the type strain RB5<sup>T</sup> (=VKM Ac-2839<sup>T</sup>=NRRL B65539<sup>T</sup>).
Project description:A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of white-nose syndrome, and described using multi-locus sequencing analysis. Swabs from both the cave myotis bat (Myotis velifer) and the Brazilian free-tailed bat (Tadarida brasiliensis) in southern New Mexico bore isolates AC536, AC541<sup>T</sup> and AC563, which were characterised using phylogenetic, morphological, and phenotypic analyses. Multi-locus sequence analysis positions AC541<sup>T</sup> with neighbors Streptomyces rubidus (NRRL B-24619<sup>T</sup>), Streptomyces guanduensis (NRRL B-24617<sup>T</sup>), and Streptomyces yeochonensis (NRRL B-24245<sup>T</sup>). A complete genome of the type strain was assembled to determine its taxonomy and secondary metabolite potential. ANI comparisons between all closely related types strains are shown to be well below the 95-96% species delineation. DNA-DNA relatedness between AC541<sup>T</sup> and its nearest neighbors ranged between 23.7 and 24.1% confirming novelty. Approximately 1.49 Mb or 17.76% of the whole genome is devoted to natural product biosynthesis. The DNA G + C content of the genomic DNA of the type strain is 73.13 mol %. Micromorphology depicts ovoid spores with smooth surfaces in flexuous chains. Strains presented an ivory to yellow hue on most ISP media except inorganic salts-starch agar (ISP4) and can grow on D-glucose, mannitol, and D-fructose, but exhibited little to no growth on L-arabinose, sucrose, D-xylose, inositol, L-rhamnose, D-raffinose, and cellulose. This clade possesses the capability to grow from 10 to 45 °C and 12.5% (w/v) NaCl. There was strain growth variation in pH, but all isolates thrive at alkaline levels. Based on our polyphasic study of AC541<sup>T</sup>, the strain warrants the assignment to a novel species, for which the name Streptomyces buecherae sp. nov. is proposed. The type strain is AC541<sup>T</sup> (= JCM 34263<sup>T</sup>, = ATCC TSD201<sup>T</sup>).
Project description:Bacterial wilt of tomato is a destructive disease caused by <i>Ralstonia solanacearum</i> throughout the world. An endophytic actinomycete with antagonistic activity, designated strain LD120<sup>T</sup>, was isolated from moss (<i>Physcomitrium sphaericum</i> (Ludw) Fuernr). The biocontrol test demonstrated that co-inoculation by the isolate and the pathogen gave the greatest biocontrol efficiency of 63.6%. Strain LD120<sup>T</sup> had morphological characteristics and chemotaxonomic properties identical to those of members of the genus <i>Streptomyces</i>. The diamino acid present in the cell wall was LL-diaminopimelic acid. Arabinose, glucose, rhamnose, and ribose occured in whole cell hydrolysates. The menaquinones detected were MK-9(H<sub>4</sub>), MK-9(H<sub>6</sub>), MK-9(H<sub>8</sub>), and MK-9(H<sub>2</sub>). The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylinositol. The major cellular fatty acids were found to be iso-C<sub>16:0</sub>, iso-C<sub>17:0</sub>, anteiso-C<sub>15:0</sub>, and C<sub>16:1</sub> ω7c. The DNA G+C content of the draft genome sequence, consisting of 7.6 Mbp, was 73.1%. Analysis of the 16S rRNA gene sequence showed that strain LD120<sup>T</sup> belongs to the genus <i>Streptomyces</i>, with the highest sequence similarity to <i>Streptomyces azureus</i> NRRL B-2655<sup>T</sup> (98.97%), but phylogenetically clustered with <i>Streptomyces anandii</i> NRRL B-3590<sup>T</sup> (98.62%). Multilocus sequence analysis based on five other house-keeping genes (<i>atpD</i>, <i>gyrB</i>, <i>rpoB</i>, <i>recA</i>, and <i>trpB)</i> and the low level of DNA-DNA relatedness, as well as phenotypic differences, allowed strain LD120<sup>T</sup> to be differentiated from its closely related strains. Therefore, the strain was concluded to represent a novel species of the genus <i>Streptomyces</i>, for which the name <i>Streptomyces</i><i>physcomitrii</i> sp. nov. was proposed. The type strain was LD120<sup>T</sup> (=CCTCC AA 2018049<sup>T</sup> = DSM 110638<sup>T</sup>).
Project description:We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s).The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules.
Project description:A novel actinobacterium, designated ASO4wet<sup>T</sup>, was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wet<sup>T</sup> is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413<sup>T</sup> (98.87 %), Streptomyces glycovorans YIM M 10366<sup>T</sup> (98.38 %), and Streptomyces abyssalis YIM M 10400<sup>T</sup> (97.53 %). Strain ASO4wet<sup>T</sup> contained MK-9(H8) as the predominant menaquinone and the major fatty acids are iso-C<sub>16:0</sub>, anteiso-C<sub>15:0</sub>, and iso-C<sub>15:0</sub>. Polyphasic taxonomy was carried out between strain ASO4wet<sup>T</sup> and its phylogenetically closely related Streptomyces strains, which further elucidated their relatedness and revealed that strain ASO4wet<sup>T</sup> could be distinguished from currently known Streptomyces species. Strain ASO4wet<sup>T</sup> clearly represents a novel species in genus Streptomyces. We propose the name Streptomyces bathyalis sp. nov., with the type strain ASO4wet<sup>T</sup> (= DSM 106605<sup>T</sup> = NCCB 100657<sup>T</sup>). Analysis of the whole-genome sequence of S. bathyalis revealed that genome size is 7,377,472 bp with 6332 coding sequences.
Project description:The taxonomy of an actinobacterial strain, designated JJY4<sup>T</sup>, was established using a polyphasic approach. JJY4<sup>T</sup> was isolated from the rhizosphere of Chromolaena odorata in Yaoundé (Cameroon) during a project for the selection of biological control agents. Strain JJY4<sup>T</sup> exhibited antimicrobial activities against bacteria, fungi, and oomycetes. Strain JJY4<sup>T</sup> also exhibited the traits of plant growth-promoting rhizobacteria such as the solubilization of inorganic phosphate, production of siderophores and indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase activity. In planta assays performed on cocoa plantlets confirmed that strain JJY4<sup>T</sup> exhibited strong abilities to promote plant growth and protect against Phytophthora megakarya, the main causal agent of cocoa pod rot. The formation of rugose-ornamented spores in spiral spore chains by strain JJY4<sup>T</sup> is a typical feature of members found in the Streptomyces violaceusniger clade and, similar to some members of the clade, strain JJY4<sup>T</sup> produces geldanamycin. A phylogenetic analysis based on 16S rRNA gene sequences confirmed this classification and suggests that strain JJY4<sup>T</sup> be added to the subclade constituted of the type strains Streptomyces malaysiensis DSM 41697<sup>T</sup> and Streptomyces samsunensis DSM 42010<sup>T</sup>. However, DNA-DNA relatedness and physiological characteristics allowed for the differentiation of strain JJY4<sup>T</sup> from its closest phylogenetic relatives. Based on these results, strain JJY4<sup>T</sup> (=NRRL B-65369, =NBRC 112705) appears to represent a novel species in the S. violaceusniger clade for which the proposed name is Streptomyces cameroonensis sp. nov.
Project description:The taxonomic positions of two novel aerobic, Gram-positive actinobacteria, designated strains RB29<sup>T</sup> and RB68<sup>T</sup>, were determined using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of RB29<sup>T</sup> were identified as <i>Actinomadura rayongensis</i> DSM 102126<sup>T</sup> (99.2 % similarity) and <i>Actinomadura atramentaria</i> DSM 43919<sup>T</sup> (98.7 %), and for strain RB68<sup>T</sup> was <i>Actinomadura hibisca</i> DSM 44148<sup>T</sup> (98.3 %). Digital DNA-DNA hybridization (dDDH) between RB29<sup>T</sup> and its closest phylogenetic neighbours, <i>A. rayongensis</i> DSM 102126<sup>T</sup> and <i>A. atramentaria</i> DSM 43919<sup>T</sup>, resulted in similarity values of 53.2 % (50.6-55.9 %) and 26.4 % (24.1-28.9 %), respectively. Additionally, the average nucleotide identity (ANI) was 93.2 % (94.0 %) for <i>A. rayongensis</i> DSM 102126<sup>T</sup> and 82.3 % (78.9 %) for <i>A. atramentaria</i> DSM 43919<sup>T</sup>. dDDH analysis between strain RB68<sup>T</sup> and <i>A. hibisca</i> DSM 44148<sup>T</sup> gave a similarity value of 24.5 % (22.2-27.0 %). Both strains, RB29<sup>T</sup> and RB68<sup>T</sup>, revealed morphological characteristics and chemotaxonomic features typical for the genus <i>Actinomadura</i>, such as the presence of <i>meso</i>-diaminopimelic acid in the cell wall, galactose and glucose as major sugar components within whole-cell hydrolysates and the absence of mycolic acids. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Predominant menaquinones were MK-9(H<sub>6</sub>) and MK-9(H<sub>8</sub>) for RB29<sup>T</sup> and MK-9(H<sub>4</sub>) and MK-9(H<sub>6</sub>) for RB68<sup>T</sup>. The main fatty acids were identified as 10-methyloctadecanoic acid (10-methyl C<sub>18:0</sub>), 14-methylpentadecanoic acid (iso-C<sub>16:0</sub>), hexadecanoic acid (C<sub>16:0</sub>) and <i>cis</i>-9-octadecanoic acid (C<sub>18 : 1</sub> ω9<i>c</i>). Here, we propose two novel species of the genus <i>Actinomadura</i>: <i>Actinomadura rubteroloni</i> sp. nov. with the type strain RB29<sup>T</sup> (=CCUG 72668<sup>T</sup>=NRRL B-65537<sup>T</sup>) and <i>Actinomadura macrotermitis</i> sp. nov. with the type strain RB68<sup>T</sup> (=CCUG 72669<sup>T</sup>=NRRL B-65538<sup>T</sup>).
Project description:Streptomyces colonosanans MUSC 93JT, a novel strain isolated from mangrove forest soil located at Sarawak, Malaysia. The bacterium was noted to be Gram-positive and to form light yellow aerial and vivid yellow substrate mycelium on ISP 2 agar. The polyphasic approach was used to determine the taxonomy of strain MUSC 93JT and the strain showed a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. Phylogenetic and 16S rRNA gene sequence analysis indicated that closely related strains include Streptomyces malachitofuscus NBRC 13059T (99.2% sequence similarity), Streptomyces misionensis NBRC 13063T (99.1%), and Streptomyces phaeoluteichromatogenes NRRL 5799T (99.1%). The DNA-DNA relatedness values between MUSC 93JT and closely related type strains ranged from 14.4 ± 0.1 to 46.2 ± 0.4%. The comparison of BOX-PCR fingerprints indicated MUSC 93JT exhibits a unique DNA profile. The genome of MUSC 93JT consists of 7,015,076 bp. The DNA G + C content was determined to be 69.90 mol%. The extract of strain MUSC 93JT was demonstrated to exhibit potent antioxidant activity via ABTS, metal chelating, and SOD assays. This extract also exhibited anticancer activity against human colon cancer cell lines without significant cytotoxic effect against human normal colon cells. Furthermore, the chemical analysis of the extract further emphasizes the strain is producing chemo-preventive related metabolites. Based on this polyphasic study of MUSC 93JT, it is concluded that this strain represents a novel species, for which the name Streptomyces colonosanans sp. nov. is proposed. The type strain is MUSC 93JT (= DSM 102042T = MCCC 1K02298T).
Project description:<i>Ralstonia solanacearum</i> is a major phytopathogenic bacterium that attacks many crops and other plants around the world. In this study, a novel actinomycete, designated strain NEAU-SSA 1<sup>T</sup>, which exhibited antibacterial activity against <i>Ralstonia solanacearum</i>, was isolated from soil collected from Mount Song and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with those of the genus <i>Streptomyces</i>. The 16S rRNA gene sequence analysis showed that the isolate was most closely related to <i>Streptomyces aureoverticillatus</i> JCM 4347<sup>T</sup> (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a cluster with <i>Streptomyces vastus</i> JCM4524<sup>T</sup> (97.4%), <i>S. cinereus</i> DSM43033<sup>T</sup> (97.2%), <i>S. xiangluensis</i> NEAU-LA29<sup>T</sup> (97.1%) and <i>S. flaveus</i> JCM3035<sup>T</sup> (97.1%). The cell wall contained <i>LL</i>-diaminopimelic acid and the whole-cell hydrolysates were ribose, mannose and galactose. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), hydroxy-phosphatidylethanolamine (OH-PE), phosphatidylinositol (PI), two phosphatidylinositol mannosides (PIMs) and an unidentified phospholipid (PL). The menaquinones were MK-9(H<sub>4</sub>), MK-9(H<sub>6</sub>), and MK-9(H<sub>8</sub>). The major fatty acids were <i>iso</i>-C<sub>17:0</sub>, C<sub>16:0</sub> and C<sub>17:1</sub> ω9c. The DNA G+C content was 69.9 mol %. However, multilocus sequence analysis (MLSA) based on five other house-keeping genes (<i>atp</i>D, <i>gyr</i>B, <i>rec</i>A, <i>rpo</i>B, and <i>trp</i>B), DNA-DNA relatedness, and physiological and biochemical data showed that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-SSA 1<sup>T</sup> should be classified as representatives of a novel species of the genus <i>Streptomyces</i>, for which the name <i>Streptomyces sporangiiformans</i> sp. nov. is proposed. The type strain is NEAU-SSA 1<sup>T</sup> (=CCTCC AA 2017028<sup>T</sup> = DSM 105692<sup>T</sup>).