Yonghaparkia Aerolata sp. nov., a Novel Member of the Genus Yonghaparkia, Isolated From Electronic Waste Associated Bioaerosols

A Gram-positive, non-motile, non-spore-forming and short rod-shaped actinomycete strain, designated GA224T, was isolated from an electronic waste associated bioaerosols. The isolate is facultatively anaerobic, which is able to grow at 25–40 ℃ (optimum 37 ℃) and pH 6.5–8.5 (optimum 8.0). The diamino acid in the cell wall of strain GA224T is 2,4-diaminobutyric acid (DAB), while major menaquinone is MK-12. The polar lipid profile is composed of diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unidentified lipid. The major cellular fatty acid is anteiso-C15:0 and iso-C16:0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GA224T fell within the genus Yonghaparkia, the highest 16S rRNA gene sequence similarity values (98.60%) being obtained with respect to Yonghaparkia alkaliphile KSL-113T. The draft genome of strain GA224T comprised 2,495,189 bp with a G+C content of 72.17 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain GA224T and phylogenetically related Yonghaparkia species were lower than 95% and 70%, respectively. Based on the phenotypic, chemotaxonomic and genomic data, strain GA224T represents a novel species, for which the name Yonghaparkia aerolata sp. nov. is proposed, with GA224T as the type strain (= GDMCC 1.2165T = JCM 34462T).

Genome-Guided Discovery of Natural Products through Multiplexed Low-Coverage Whole-Genome Sequencing of Soil Actinomycetes on Oxford Nanopore Flongle

Short-read sequencing of GC-rich genomes such as those from actinomycetes results in a fragmented genome assembly and truncated biosynthetic gene clusters (often 10 to >100 kb long), which hinders our ability to understand the biosynthetic potential of a given strain and predict the molecules that can be produced. The current study demonstrates that contiguous DNA assemblies, suitable for analysis of BGCs, can be obtained through low-coverage, multiplexed sequencing on Flongle, which provides a new low-cost workflow ($30 to 40 per strain) for sequencing actinomycete strain libraries.

Prauserella cavernicola sp. nov., isolated from cave rock

A novel actinomycete, designated strain ASG 168T, was isolated from cave rock collected from Stegodon Sea Cave in Thailand. Long chains of non-motile spores that were oval or spherical in shape with a smooth surface developed on aerial mycelia. Substrate mycelia fragmented into irregular rod-shaped elements. A polyphasic taxonomic study showed that strain ASG 168T had typical characteristics of members of the genus Prauserella . 16S rRNA gene sequence analysis indicated that strain ASG 168T shared 97.5 % similarity with Prauserella marina MS498T and 96.7 % with Prauserella coralliicola SCSIO 11529T. Average nucleotide identity values with P. coralliicola SCSIO 11529T and P. marina MS498T were 82.98 and 76.08 %, respectively. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose, arabinose and galactose. The predominant menaquinone was MK-9(H4). The predominant fatty acids were iso-C16 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The phospholipid profile consisted of phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 70.6 mol%. Differentiation of strain ASG 168T from closely related species was evident from digital DNA–DNA hybridization values of 29.2 and 21.3 % with P. coralliicola and P. marina , respectively. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, the novel actinomycete strain ASG 168T (=TBRC 13679T=NBRC 114887T) is proposed to be the type strain of a novel species, Prauserella cavernicola sp. nov.

Development of an agar-plug cultivation system for bioactivity assays of actinomycete strain collections

Natural products are an important source of lead compounds for the development of drug substances. Actinomycetes have been valuable especially for the discovery of antibiotics. Increasing occurrence of antibiotic resistance among bacterial pathogens has revived the interest in actinomycete natural product research. Actinobacteria produce a different set of natural products when cultivated on solid growth media compared with submersed culture. Bioactivity assays involving solid media (e.g. agar-plug assays) require manual manipulation of the strains and agar plugs. This is less convenient for the screening of larger strain collections of several hundred or thousand strains. Thus, the aim of this study was to develop a 96-well microplate-based system suitable for the screening of actinomycete strain collections in agar-plug assays. We developed a medium-throughput cultivation and agar-plug assay workflow that allows the convenient inoculation of solid agar plugs with actinomycete spore suspensions from a strain collection, and the transfer of the agar plugs to petri dishes to conduct agar-plug bioactivity assays. The development steps as well as the challenges that were overcome during the development (e.g. system sterility, handling of the agar plugs) are described. We present the results from one exemplary screening campaign targeted to identify compounds inhibiting Agr-based quorum sensing where the workflow was used successfully. We present a novel and convenient workflow to combine agar diffusion assays with microtiter-plate-based cultivation systems in which strains can grow on a solid surface. This workflow facilitates and speeds up the initial medium throughput screening of natural product-producing actinomycete strain collections against monitor strains in agar-plug assays.

Two new α-Methoxy-γ-Pyrones From the Mangrove Sediment-Derived Streptomyces psammoticus SCSIO NS126

Two new α-methoxy- γ-pyrone analogs, 2-methoxy-3-methyl-5,6-diethyl- γ-pyrone (2) and 2-methoxy-3,5-dimethyl-6-propyl- γ-pyrone (3), together with 2-methoxy-3,5-dimethyl-6-ethyl- γ-pyrone (1), firstly isolated from natural sources, were obtained from the EtOAc-solube extract of the mangrove sediment-derived actinomycete strain Streptomyces psammoticus SCSIO NS126, under the optimized fermentation conditions. Their structures were elucidated by detailed spectroscopic analysis and by comparison of their spectroscopic data with those reported in the literature. Those α-methoxy-γ-pyrones were evaluated for their acetylcholinesterase inhibitory activity; however, none of them exhibited obvious activity. Moreover, their biosynthetic relationship with piericidins was also discussed.

Cytotoxic Minor Piericidin Derivatives from the Actinomycete Strain Streptomyces psammoticus SCSIO NS126

The mangrove-sediment-derived actinomycete strain Streptomyces psammoticus SCSIO NS126 was found to have productive piericidin metabolites featuring anti-renal cell carcinoma activities. In this study, in order to explore more diverse piericidin derivatives, and therefore to discover superior anti-tumor lead compounds, the NS126 strain was further fermented at a 300-L scale under optimized fermentation conditions. As a result, eight new minor piericidin derivatives (piericidins L-R (1–7) and 11-demethyl-glucopiericidin A (8)) were obtained, along with glucopiericidin B (9). The new structures including absolute configurations were determined by spectroscopic methods coupled with experimental and calculated electronic circular dichroism. We also proposed plausible biosynthetic pathways for these unusual post-modified piericidins. Compounds 1 and 6 showed selective cytotoxic activities against OS-RC-2 cells, and 2–5 exhibited potent cytotoxicity against HL-60 cells, with IC50 values lower than 0.1 μM. The new piericidin glycoside 8 was cytotoxic against ACHN, HL-60 and K562, with IC50 values of 2.3, 1.3 and 5.5 μM, respectively. The ability to arrest the cell cycle and cell apoptosis effects induced by 1 and 6 in OS-RC-2 cells, 2 in HL-60 cells, and 8 in ACHN cells were then further investigated. This study enriched the structural diversity of piericidin derivatives and confirmed that piericidins deserve further investigations as promising anti-tumor agents.

Studying on the antifungal activityof the actinomycete XK1 isolatedfrom growing orange’s soil against pathogenic fungi causing disease in citrus

Streptomyces are considered to be one of the actinomycetes genera having potential in the production of agricultural probiotics because they are safe and have strong antagonism to many bacterial and fungal species that cause plant diseases. In this study, 18 strains of actinomycetes were isolated from growing oranges’ soil in Ha Giang province, of which the actinomycete strain XK1 was considered to be strongly resistant to the fungi Penicillium digitatum and Colletotrichum gloeosporioides causing fruit rot and shedding in citrus. Based on morphological characteristics and 16S rRNA sequence, the strain XK1 was determined to belong to the Streptomyces albulus. On MT2 medium with pH=6, after five days of shaking cultivation at 30°C, the liquid cultures of S. albulus XK1 showed the strongest resisting activity to P. digitatum and C. gloeosporioides. At the same time, the broth cultures of S. albulus XK1 showed inhibitory activity against P. digitatum in oranges. The actinomycete strain S. albulus XK1 was selected base on strong antifungal ability against P. digitatum and C. gloeosporioides and had a potential for application in the production of probiotics used to control fruit rot and shedding in citrus.

Abyssomicins—A 20-Year Retrospective View

Abyssomicins represent a new family of polycyclic macrolactones. The first described compounds of the abyssomicin family were abyssomicin B, C, atrop-C, and D, produced by the marine actinomycete strain Verrucosispora maris AB-18-032, which was isolated from a sediment collected in the Sea of Japan. Among the described abyssomicins, only abyssomicin C and atrop-abyssomicin C show a high antibiotic activity against Gram-positive bacteria, including multi-resistant and vancomycin-resistant strains. The inhibitory activity is caused by a selective inhibition of the enzyme 4-amino-4-deoxychorismate synthase, which catalyzes the transformation of chorismate to para-aminobenzoic acid, an intermediate in the folic acid pathway.

Actinomycete strain type determines the monodispersity and antibacterial properties of biogenically synthesized silver nanoparticles

Background Bio-nanotechnology is considered as one of the low-cost approaches that have been utilized in production of nanomaterials. The current research aimed at investigating the influence of different types of Actinomycete strains on the final properties of silver nanoparticles (AgNPs) such as size, shape, polydispersity, and antibacterial properties. For this purpose, the following techniques were employed UV spectrophotometer, SDS-PAGE electrophoresis, TEM, FTIR, antibacterial agar diffusion test, and Zetasizer. Results It was found that among 34 Streptomyces isolates collected from the soil, Streptomyces spiralis and Streptomyces rochei were able to reduce silver nitrate into sliver nanoparticles. The diversity and molecular weights of extracellular proteins secreted by these stains were different as proved by SDS-PAGE technique. This consequently resulted in differences in polydispersity of AgNPs which indicate that the sizes of AgNPs were highly dependent on the amount, molecular sizes, and diversity of extracellular matrix proteins of the microorganism. Conclusion This article might give an insight about the importance of molecular sizes of biomacromolecules such as proteins on the physical properties of biogenic synthesized nanoparticles.