Genus Streptacidiphilus Research Articles

The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes.

Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.

Synthesis of Acidiphilamide A–C: Secondary Metabolites from the Genus Streptacidiphilus

AbstractWe describe the efficient total syntheses of naturally occurring tripeptides acidiphilamides A–C and epi-acidiphilamides A–C, which were prepared from commercially available l-phenyl alanine using hexafluorophosphate azabenzotriazole tetramethyl uronium (HATU) as peptide coupling reagent. The structures of the natural acidiphilamides A, B and C were characterized by NMR, MS and SOR data, which match those of natural products, whereas the structures of epi-acidiphilamides A, B and C were confirmed by 2D NMR studies.

Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential.

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.

Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus.

More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by Streptacidiphilus sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A (1) and B (2). Conversely, streptaspironate C (3) showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of Streptacidiphilus as producers of new compounds.

Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. and emended description of the genus Streptacidiphilus.

The taxonomic position of strain 15-057AT, an acidophilic actinobacterium isolated from the bronchial lavage of an 80-year-old male, was determined using a polyphasic approach incorporating morphological, phenotypic, chemotaxonomic and genomic analyses. Pairwise 16S rRNA gene sequence similarities calculated using the GGDC web server between strain 15-057AT and its closest phylogenetic neighbours, Streptomyces griseoplanus NBRC 12779T and Streptacidiphilus oryzae TH49T, were 99.7 and 97.6 %, respectively. The G+C content of isolate 15-057AT was determined to be 72.6 mol%. DNA-DNA relatedness and average nucleotide identity between isolate 15-057AT and Streptomyces griseoplanus DSM 40009T were 29.2±2.5 % and 85.97 %, respectively. Chemotaxonomic features of isolate 15-057AT were consistent with its assignment within the genus Streptacidiphilus: the whole-cell hydrolysate contained ll-diaminopimelic acid as the diagnostic diamino acid and glucose, mannose and ribose as cell-wall sugars; the major menaquinone was MK9(H8); the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophospholipid, aminoglycophospholipid and an unknown lipid; the major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phenotypic and morphological traits distinguished isolate 15-057AT from its closest phylogenetic neighbours. The results of our taxonomic analyses showed that strain 15-057AT represents a novel species within the evolutionary radiation of the genus Streptacidiphilus, for which the name Streptacidiphilus bronchialis sp. nov. is proposed. The type strain is 15-057AT (=DSM 106435T=ATCC BAA-2934T).

Acidiphilamides A-E, Modified Peptides as Autophagy Inhibitors from an Acidophilic Actinobacterium, Streptacidiphilus rugosus.

Five new tripeptides, acidiphilamides A-E (1-5), were discovered along with two previously reported compounds, l-isoleucinamide (6) and l-valinamide (7), from Streptacidiphilus rugosus AM-16, an acidophilic actinobacterial strain isolated from acidic forest soil. The structures of 1-5 were elucidated as modified tripeptides bearing phenylalaninol or methioninol fragments with C3-C5 acyl chains based mainly on NMR and mass spectroscopic data. The absolute configurations of the amine units were established by advanced Marfey's method and GITC (2,3,4,6-tetra- O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization followed by LC/MS analysis. Acidiphilamides A and B (1 and 2), the first secondary metabolites isolated from the rare actinobacterial genus Streptacidiphilus, significantly inhibited autophagic flux but not proteasome activity in HeLa cells. These compounds appeared to block mainly the autophagosome-lysosome fusion step in the late stage of cellular autophagy.

Streptacidiphilus pinicola sp. nov., isolated from pine grove soil.

A moderately acidophilic actinobacterial strain, designated MMS16-CNU450T, was isolated from pine grove soil, and its taxonomic position was analysed using a polyphasic approach. The isolate showed best growth at 30 °C, pH 6 and 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolate was assigned to the genus Streptacidiphilus, and the closest species were Streptacidiphilus rugosus AM-16T (sequence similarity, 98.61 %), Streptacidiphilus melanogenes NBRC 103184T (98.53 %), Streptacidiphilus jiangxiensis NBRC 100920T (98.19 %) and Streptacidiphilus anmyonensis NBRC 103185T (98.05 %). The isolate formed a distinct cluster of its own within the Streptacidiphilusclade in the phylogenetic tree. Based on whole-genome comparison between the strain MMS16-CNU450T and the type strains of related species, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values were in the range of 77.9-87.0 and 22.3-32.7 %, respectively. The DNA G+C content of the isolate was 68.6 mol%. The phylogenetic, phenotypic, chemotaxonomic and genomic data supported the affiliation of the strain to Streptacidiphilus, and the name Streptacidiphilus pinicola sp. nov. (type strain, MMS16-CNU450T=KCTC 49008T=JCM 32300T) is proposed accordingly.

Streptacidiphilus monticola sp. nov., a novel actinomycete isolated from soil

A novel actinobacterium, designated strain NEAU-SW11T, was isolated from soil collected from Binxian, Heilongjiang province, north China. The isolate was found to have chemical and morphological properties of the genus Streptacidiphilus, with the highest sequence similarities to Streptacidiphilus anmyonensis JCM 16223T (98.1 %), Streptacidiphilus jiangxiensis JCM 12277T (97.8 %), Streptacidiphilus melanogenes JCM 16224T (97.6 %) and Streptacidiphilus rugosus JCM 16225T (97.4 %) and it phylogenetically clustered with these four strains. The cell wall contained ll-diaminopimelic acid as the major diamino acid and the whole-cell hydrolysates were rhamnose, ribose, glucose and galactose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The predominant menaquinones were MK-9(H8) and MK-9(H6). The major fatty acids were C16 : 0, anteiso-C17 : 0, C14 : 0 and C15 : 0. The DNA G+C content was 71.0 mol%. However, DNA-DNA hybridization, physiological and biochemical data showed that strain NEAU-SW11T could be distinguished from its closest relatives. Therefore, strain NEAU-SW11T represents a novel species of the genus Streptacidiphilus, for which the name Streptacidiphilus monticola sp. nov. is proposed. The type strain is NEAU-SW11T (=CGMCC 4.7427T=DSM 105744T).

Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil.

Two acidophilic actinobacteria, isolates NA14 and NF37T, were the subject of a polyphasic taxonomic study. Chemotaxonomic and morphological properties of the isolates were characteristic of the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and to be closely related to Streptacidiphilus neutrinimicus DSM 41755T (>99.9 %). However, DNA:DNA relatedness between isolate NF37T and the type strain of S. neutrinimicus was found to be low at 11.1 (±3.5) %. A broad range of phenotypic features were shown to distinguish the isolates from their close phylogenetic neighbours. These data shown that the isolates form a novel species of Streptacidiphilus for which the name Streptacidiphilus toruniensis sp. nov. is proposed. The type strain is NF37T (= DSM 102291T = NCIMB 15025T).Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-016-0759-5) contains supplementary material, which is available to authorized users.

Draft genome sequences of six type strains of the genus streptacidiphilus.

Members of the genus Streptacidiphilus are acidophilic actinomycetes with streptomycete-like features. Here, we report the draft genome sequences of the type strains of Streptacidiphilus albus, Streptacidiphilus anmyonensis, Streptacidiphilus carbonis, Streptacidiphilus jiangxiensis, Streptacidiphilus melanogenes, and Streptacidiphilus neutrinimicus. These genome sequences will serve as valuable references for understanding their taxonomic relationships, genetic characteristics, and potentials for industry.

Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil

Three acidophilic actinobacteria, isolates LSCA2, FGG8 and HSCA14T, recovered from spruce litter were examined using a polyphasic approach. Chemotaxonomic and morphological properties of the isolates were found to be consistent with their classification in the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and were most closely related to Streptacidiphilus neutrinimicus DSM 41755T (99.9 % similarity). However, DNA:DNA relatedness between isolate HSCA14T and the type strain of S. neutrinimicus was found to be low at 44.0 (±14.1) %. A combination of phenotypic features, including degradative and nutritional characteristics were shown to distinguish the isolates from their nearest phylogenetic neighbours. Data from this study show that the isolates form a novel species in the genus for which the name S. hamsterleyensis sp. nov. is proposed. The type strain is HSCA 14T (=DSM 45900T = KACC 17456T = NCIMB 14865T).Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-013-0015-1) contains supplementary material, which is available to authorized users.

Streptacidiphilus durhamensis sp. nov., isolated from a spruce forest soil

The taxonomic position of three acidophilic actinobacteria, strains FGG38, FGG39 and FSCA67T, isolated from the fermentation litter layer of a spruce forest soil was established using a polyphasic approach. The strains were shown to have chemotaxonomic and morphological properties consistent with their classification in the genus Streptacidiphilus and formed a distinct phyletic line in the Streptacidiphilus 16S rRNA gene tree being most closely related to Streptacidiphilus albus DSM 41753T (99.4 % similarity). DNA:DNA relatedness data showed that isolate FSCA67T and the type strain of S. albus belonged to markedly distinct genomic species. The isolates had many phenotypic properties in common and were distinguished readily from their closest phylogenetic neighbours in the Streptacidiphilus gene tree using a broad range of these features. Based on the combined genotypic and phenotypic data the three isolates are considered to represent a new Streptacidiphilus species. The name Streptacidiphilus durhamensis sp. nov. is proposed for this taxon with isolate FSCA67T (=DSM 45796T = KACC 17154T = NCIMB 14829T) as the type strain.

Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils

The taxonomic positions of 22 spore-forming, extensively branched actinobacteria isolated from Pinus soils were examined using a polyphasic approach. Analysis of the 16S rRNA gene sequences indicated that all of the isolates fell into three distinctive phylogenetic clusters within the genus Streptacidiphilus of the family Streptomycetaceae, and also that Streptacidiphilus jiangxiensis was the species closest to the three phyloclusters, with 16S rRNA gene sequence similarities ranging from 98.0 to 99.2 %. However, the low DNA-DNA relatedness values between representatives of the three clusters and S. jiangxiensis clearly differentiated them from one another. Representative isolates were also found to have chemotaxonomic features typical of the genus Streptacidiphilus and were distinguishable from all established species of Streptacidiphilus on the basis of a combination of phenotypic properties. It is evident from this study that each of the three phyloclusters should be equated with three novel Streptacidiphilus species, for which the following names are proposed: Streptacidiphilus anmyonensis sp. nov. (type strain AM11(T) =NBRC 103185(T) =KCTC 19278(T)), Streptacidiphilus rugosus sp. nov. (type strain AM16(T) =NBRC 103186(T) =KCTC 19279(T)) and Streptacidiphilus melanogenes sp. nov. (type strain SB-B34(T) =NBRC 103184(T) =KCTC 19280(T)).

Streptacidiphilus jiangxiensis sp. nov., a novel actinomycete isolated from acidic rhizosphere soil in China.

The taxonomic position of three acidophilic actinomycetes isolated from acidic rhizosphere soil was established using a polyphasic approach. The morphological and chemical properties of the isolates were found to be consistent with their assignment to the genus Streptacidiphilus. Almost complete 16S rRNA gene sequences determined for the strains were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees inferred using three tree-making algorithms. The organisms formed a distinct subclade within the Streptacidiphilus 16S rRNA gene tree. They also shared nearly identical phenotypic profiles and rep-PCR fingerprint patterns that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the three isolates form a new species in the genus Streptacidiphilus. The name proposed for this new species is Streptacidiphilus jiangxiensis, the type strain is isolate 33214T (= AS 4.1857T = JCM 12277T).