Streptomyces: The biofactory of secondary metabolites

Biocontrol potential of Streptomyces sp. N2 against green and blue mold disease in postharvest navel orange and the action mechanism

The objective of this study was to provide a promising alternative to chemical fungicides for management of postharvest citrus decay, thereby promoting sustainable citrus fruit production. The postharvest decay of citrus fruit caused by Penicillium digitatum and Penicillium italicum results in substantial economic losses in citrus industry worldwide. With growing fungal resistance issues in P. digitatum and P. italicum, there is an urgent need for searching new methods to address above problems in a safe and environmentally friendly way. Streptomyces sp. N2, a new species from Streptomyces genus, exhibits significant antagonistic activity against Rhizoctonia solani. However, its biocontrol efficacy against postharvest decay caused by P. digitatum and P. italicum and its action mechanism remain unknown. In this study, Streptomyces sp. N2 was found to have significant potential in controlling green and blue mold diseases in postharvest navel oranges. Moreover, the action mechanism of Streptomyces sp. N2 against both P. italicum and P. digitatum was elucidated. On the one hand, Streptomyces sp. N2 stimulated fruit resistance to fight against invading fungal pathogens. It significantly reduced ROS content in navel orange upon the infection of mold disease, increased the production of defense-related enzymes including peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) and pathogenesis-related proteins of chitinase and β-1,3-glucanase. On the other hand, Streptomyces sp. N2 secreted bioactive substances to inhibit the growth of P. italicum and P. digitatum so as to prevent the development of postharvest decay. The bioactive substances secreted by Streptomyces sp. N2 significantly inhibited the spore germination and mycelial growth and led to microstructural damages to the cell wall and membrane, ROS burst, and mitochondrial dysfunction in both P. italicum and P. digitatum. This study provides a theoretical reference and application potential for the biological control of Streptomyces sp. N2 on green and blue mold diseases.

The faucet knob effect of DptE crotonylation on the initial flow of daptomycin biosynthesis

We propose here that acylation modification of actinomycete proteins is a restrictive system that limits the excessive synthesis of secondary metabolites, its mechanism has not been clearly elucidated before. We used crotonylation as an example to investigate the acylation effect in the daptomycin biosynthesis by Streptomyces roseosporus. Our experiments revealed abundant crotonylation of numerous secondary metabolic enzymes in Streptomyces roseosporus, a daptomycin producer. DptE, which initiates daptomycin biosynthesis, is crotonylated at K454. We experimentally identified the corresponding DptE crotonyltransferase Kct1 and decrotonylase CobB. Further studies consistently confirmed that decrotonylation increases DptE activity. Decrotonylation functions like loosening a faucet knob, increasing substrate channel throughput and the initial flow of daptomycin biosynthesis. Moreover, DptE catalytic activity was enhanced via K454 and neighboring residues K184 and Q420 mutation, increasing daptomycin yield by 132%; daptomycin biosynthesis related metabolism activities also increased. Substrate channel prediction revealed 38% higher throughput for mutant DptE (K454I/K184Q/Q420N) than crotonylated DptE. Molecular dynamics (MD) simulations revealed significant increases in flexibility and substrate affinity of the mutant. In summary, we elucidated the faucet knob effect of DptE crotonylation on the initial flow of daptomycin biosynthesis and adopted decrotonylation to generate high-yield industrial strains.

Mitigating genetic instability caused by the excision activity of the phiC31 integrase in Streptomyces

Over the past three decades, the integrase (Int) from Streptomyces phage phiC31 has become a valuable genome engineering tool across various species. phiC31 Int was thought to mediate unidirectional site-specific integration (attP × attB to attL and attR) in the absence of the phage-encoded recombination directionality factor (RDF). However, we have shown in this study that Int can also catalyze reverse excision (attL × attR to attP and attB) at low frequencies in Streptomyces lividans and Escherichia coli, causing genetic instability in engineered strains. To address this issue, we developed a two-plasmid co-conjugation (TPC) system. This system consists of an attP-containing integration vector and an Int expression suicide plasmid, both carrying oriT to facilitate efficient conjugation transfer from E. coli to Streptomyces. Using the TPC system, genetically stable integrants free of Int can be generated quickly and easily. The indigoidine-producing strains generated by the TPC system exhibited higher genetic stability and production efficiency compared to the indigoidine-producing strain generated by the conventional integration system, further demonstrating the utility of the TPC system in the field of biotechnology. We anticipate that the strategies presented here will be widely adopted for stable genetic engineering of industrial microbes using phage integrase-based integration systems.IMPORTANCELarge serine recombinases (LSRs), including the bacteriophage phiC31 integrase, were previously thought to allow only unidirectional site-specific integration (attP × attB to attL and attR). Our study is the first to show that the phiC31 integrase can also catalyze a low-efficiency reverse excision reaction in Streptomyces and E. coli without the involvement of the phage-encoded recombination directionality factor (RDF). The genetic instability caused by the low in vivo excisionase activity of the phiC31 integrase is a major challenge for biotechnological applications. Our study addresses this issue by developing a two-plasmid co-conjugation (TPC) system that facilitates the construction of Int-deficient genomic engineering strains. The Int-deficient integrants produced by this TPC system exhibit strong genetic stability for introduced genes and maintain stable production traits even in the absence of selection pressure, making them highly valuable for industrial applications.

Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove

A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.

Olikomycin A-A Novel Calcium-Dependent Lipopeptide with Antibiotic Activity Against Multidrug-Resistant Bacteria

Research into new antibiotics is becoming increasingly important as antibiotic resistance increases worldwide. The genus Streptomyces in particular is able to produce a wide range of antimicrobial products due to the large number of biosynthetic gene clusters (BGCs) in its genome. However, not all BGCs are expressed under laboratory conditions. In this work, deletion of the gene wblA, encoding a global regulator of natural product biosynthesis and morphogenesis in Streptomyces, led to the production of a novel natural product, olikomycin A, in Streptomyces ghanaensis ATCC 14672. Complete structure elucidation revealed that olikomycin A belongs to a class of calcium-dependent antibiotics known as non-ribosomal peptide synthetase (NRPS)-encoded acidic lipopeptides. These compounds exhibit remarkable antimicrobial activity in the presence of calcium. Insights into olikomycin A biosynthesis were provided by whole genome sequencing and gene inactivation studies, while bioactivity assays showed strong inhibition of the growth of multidrug-resistant Gram-positive pathogens via disrupting cell membrane integrity. Olikomycin A shows an antibiotic profile similar to that of daptomycin, which is already in clinical use.

Streptomyces albidocamelliae sp. nov., an endophytic actinomycete isolated from the leaves of Camellia oleifera

A novel actinobacterium strain, HUAS 14-6T, was isolated from the healthy leaves of Camellia oleifera collected from Changde City, Hunan Province, China. Strain HUAS 14-6T produced tight spiral spore chains consisting of oval or spherical spores with a smooth surface. 16S rRNA gene sequence analysis revealed that strain HUAS 14-6T belonged to the genus Streptomyces and shared highest similarity to Streptomyces bungoensis DSM 41781T (99.72%). Phylogenetic analysis based on 16S rRNA gene sequences indicated strain HUAS 14-6T was in a clade with S. bungoensis DSM 41781T. However, the ANIm and dDDH between strain HUAS 14-6T and S. bungoensis DSM 41781T were 88.16% and 31.2%, respectively, far less than the species-level thresholds. Phylogenetic trees based on the five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that strain HUAS 14-6T formed a separate branch, indicating that this strain could belong to a potential new species. Pairwise MLSA distances between strain HUAS 14-6T and all type strains exhibiting 16S rRNA gene sequence similarities of ≥98.7% to it were much higher than the maximum range of 0.014 recommended for delineating a new Streptomyces species. Based on polyphasic taxonomic study, HUAS 14-6T represents a novel species within the genus Streptomyces for which the name Streptomyces albidocamelliae sp. nov. is proposed. The type strain is HUAS 14-6T (=MCCC 1K08365T=JCM 35920T).

Functional analysis of the whole CYPome and Fdxome of Streptomyces venezuelae ATCC 15439

Cytochrome P450 enzymes (CYPs or P450s) and ferredoxins (Fdxs) are ubiquitously distributed in all domains of life. Bacterial P450s are capable of catalyzing various oxidative reactions with two electrons usually donated by Fdxs. Particularly in Streptomyces, there are abundant P450s that have exhibited outstanding biosynthetic capacity of bioactive metabolites and great potential for xenobiotic metabolisms. However, no systematic study has been conducted on physiological functions of the whole cytochrome P450 complement (CYPome) and ferredoxin complement (Fdxome) of any Streptomyces strain to date, leaving a significant knowledge gap in microbial functional genomics. Herein, we functionally analyze the whole CYPome and Fdxome of Streptomyces venezuelae ATCC 15439 by investigating groups of single and sequential P450 deletion mutants, single P450 overexpression mutants, and Fdx gene deletion or repression mutants. Construction of an unprecedented P450-null mutant strain indicates that none of P450 genes are essential for S. venezuelae in maintaining its survival and normal morphology. The non-housekeeping Fdx1 and housekeeping Fdx3 not only jointly support the cellular activity of the prototypic P450 enzyme PikC, but also play significant regulatory functions. These findings significantly advance the understandings of the native functionality of P450s and Fdxs as well as their cellular interactions.

Unveiling detoxifying symbiosis and dietary influence on the Southern green shield bug microbiota

The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crops and poses a threat to global food production. Insects live in close relationships with microorganisms providing their host with unique capabilities, such as resistance to toxic plant metabolites. In this study, we investigated the resistance to and detoxification of the plant metabolite 3-nitropropionic acid (NPA) by core and transient members of the N. viridula microbial community. Microbial community members showed a different tolerance to the toxin and we determined that six out of eight strains detoxified NPA. Additionally, we determined that NPA might interfere with the biosynthesis and transport of l-leucine. Moreover, our study explored the influence of diet on the gut microbial composition of N. viridula, demonstrating that switching to a single-plant diet shifts the abundance of core microbes. In line with this, testing pairwise microbial interactions revealed that core microbiota members support each other and repress the growth of transient microorganisms. With this work, we provide novel insights into the factors shaping the insect gut microbial communities and demonstrate that N. viridula harbours many toxin-degrading bacteria that could support its resistance to plant defences.

Three New Depsipeptides, Homiamides A-C, Isolated from Streptomyces sp., ROA-065

Three new depsipeptides, homiamides A-C (1-3), were isolated from a marine sediment-derived strain of Streptomyces sp., ROA-065. The planar structures of homiamides A-C (1-3) were elucidated using mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopic data. The absolute configurations of 1-3 were deduced from the application of the Marfey's method and GC-MS analysis after formation of the O-trifluoroacetylated (S)-(+)-methyl-2-butyl ester derivatives of amino acids. Compounds 1-3 exhibited weak anti-bacterial activities against both Gram-positive bacteria and Gram-negative bacteria, with compound 1 showing MIC values of 32-64 μg/mL. In antifouling assays, compounds 1 and 2 displayed moderate activity against Micrococcus luteus KCTC 3063, while compound 3 exhibited weak activity against all tested bacteria.

An Overview of Lsr2 Repressor Effect in Streptomyces spp. Secondary Metabolism

The genus Streptomyces is one of the largest producers of secondary metabolites with bioactive properties of interest. However, many of the genes involved in synthesizing these compounds are silenced under laboratory conditions. One of the strategies used to activate these metabolic pathways is the elimination of repressor genes, which prevent the transcription of other genes. In this work, the lsr2 gene has been selected for study since it is a repressor with a preference for binding to AT-rich regions, which makes it exert its effect especially on those horizontally transferred gene sequences that have a very different GC content to the core Streptomyces spp. genome. Therefore, the effects of the deletion of this gene are observed, and, in addition, a mapping of the potential binding sites of Lsr2 in Streptomyces spp. genomes is proposed. As a result of this gene knockout, the production of various secondary metabolites is overproduced and/or activated, which suggests that the study of this regulator can be interesting in the field of natural product discovery.

Harnessing Biocontrol Potential of Streptomyces rochei Against Pythium aphanidermatum: Efficacy and Mechanisms

Tomato (Solanum lycopersicum) and chilli (Capsicum annuum) are globally significant vegetable crops susceptible to damping-off disease caused by Pythium aphanidermatum, leading to substantial yield losses. The study aimed to document the biocontrol and plant growth promotion potential of Streptomyces rochei against damping-off disease in tomato and chilli. The actinobacterial isolates ACS18 followed by ACT30, and AOE12 were accomplished as the most effective antagonists against P. aphanidermatum in vitro. Molecular characterization confirmed these isolates as members of Streptomyces genus, with ASH 18 the top performer identified as S. rochei isolate. Analysis of biomolecule through GC-MS during ditrophic interaction between pathogen and S. rochei showed the presence of various antifungal metabolites which were directly related to suppression of the pathogen. Subsequently, S. rochei was formulated into a talc-based preparation and used as seed treatment and soil application against damping-off. In greenhouse trials, significant reductions in damping-off incidence were observed, Furthermore, seedlings treated with S. rochei displayed enhanced root and shoot lengths compared to the uninoculated controls. These benefits potentiate S. rochei as a promising biocontrol agent and demonstrating its dual benefits of disease suppression and promotion of seedling growth.

Antibacterial, Herbicidal, and Plant Growth-Promoting Properties of Streptomyces sp. STD57 from the Rhizosphere of Adenophora stricta

Bacterial wilt triggered by the soil-borne pathogenic bacterium Ralstonia solanacearum is one of the most serious diseases in tomato plants, leading to huge economic losses worldwide. Biological control is considered an environmentally friendly and sustainable way to manage soil-borne diseases. In this study, Streptomyces sp. STD57 isolated from the rhizosphere of Adenophora stricta showed strong antibacterial activity against R. solanacearum. Pot experiments showed that strain STD57 exhibited a significant biocontrol effect (81.7%) on tomato bacterial wilt in the greenhouse environment. Furthermore, strain STD57 could inhibit the growth of weeds (Amaranthus retroflexus, Portulaca oleracea, and Echinochloa crusgalli) but promote the growth of crops (wheat, rice, and tomato). The plant growth-promoting substance was identified as indoleacetic acid (IAA) by high-pressure liquid chromatography-mass spectrometry and genome analysis. Coarse separation of the fermented extracts revealed that the antibacterial and herbicidal substances were mainly in the fermentation supernatant and belonged to different products. These findings suggested that strain STD57 may be a potential biocontrol and bioherbicide agent useful in agriculture.

Conjugation Mediates Large-Scale Chromosomal Transfer in Streptomyces Driving Diversification of Antibiotic Biosynthetic Gene Clusters

Streptomyces are ubiquitous soil-dwelling bacteria with large, linear genomes that are of special importance as a source of metabolites used in human and veterinary medicine, agronomy, and industry. Conjugative elements (actinomycetes integrative and conjugative elements, AICEs) are the main drivers of Streptomyces Horizontal Gene Transfer. AICE transfer has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains of Streptomyces result in the large-scale, genome-wide distributed replacement of up to one-third of the recipient chromosome, a phenomenon for which we propose the name "Streptomyces Chromosomal Transfer" (SCT). Such chromosome blending results in the acquisition, loss, and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated specialized metabolite biosynthesis gene cluster diversification holds great promise in the discovery of new bioactive compounds including antibiotics.

Exploring Xenorhabdus and Photorhabdus Nematode Symbionts in Search of Novel Therapeutics

Xenorhabdus and Photorhabdus bacteria, which live in mutualistic symbiosis with entomopathogenic nematodes, are currently recognised as an important source of bioactive compounds. During their extraordinary life cycle, these bacteria are capable of fine regulation of mutualism and pathogenesis towards two different hosts, a nematode and a wide range of insect species, respectively. Consequently, survival in a specific ecological niche favours the richness of biosynthetic gene clusters and respective metabolites with a specific structure and function, providing templates for uncovering new agrochemicals and therapeutics. To date, numerous studies have been published on the genetic ability of Xenorhabdus and Photorhabdus bacteria to produce biosynthetic novelty as well as distinctive classes of their metabolites with their activity and mechanism of action. Research shows diverse techniques and approaches that can lead to the discovery of new natural products, such as extract-based analysis, genetic engineering, and genomics linked with metabolomics. Importantly, the exploration of members of the Xenorhabdus and Photorhabdus genera has led to encouraging developments in compounds that exhibit pharmaceutically important properties, including antibiotics that act against Gram- bacteria, which are extremely difficult to find. This article focuses on recent advances in the discovery of natural products derived from these nematophilic bacteria, with special attention paid to new valuable leads for therapeutics.

New CYP154C4 from Streptomyces cavourensis YBQ59 performs regio- and stereo- selective 3β-hydroxlation of nootkatone

Nootkatone, a sesquiterpenoid widely used in the food and cosmetics industries, exhibits diverse biological activities and pharmaceutical prospects. Modification of nootkatone to create new derivatives with desirable activities has attracted significant attention. For this purpose, cytochrome P450 monooxygenases (P450 or CYP) are attractive candidates due to their ability to perform regio- and stereoselective hydroxylation at allylic C-H bonds. In this study, CYP154C4 from Streptomyces cavourensis YBQ59 was cloned and expressed in Escherichia coli. By screening 64 candidate substrates, this P450 was found to catalyze the regio- and stereoselective hydroxylation of nootkatone, yielding a single product, 3β-hydroxynootkatone. Using a whole-cell E. coli system expressing CYP154C4, supported by the heterologous redox partners YkuN from Bacillus subtilis and FdR from E. coli, 3β-hydroxynootkatone was produced on a preparative scale. The structure of this compound was determined by 1H NMR, 13C NMR, NOESY, HMBC, and HSQC. The kinetics of product formation were analyzed using HPLC, and the Km and Kcat values were calculated. Furthermore, structural insights into the selective hydroxylation of nootkatone were elucidated by molecular docking. 3β-Hydroxynootkatone, recently synthesized semi-synthetically from nootkatone, has been reported to exhibit a higher insecticidal activity than its parent compound. Additionally, the functionalization of nootkatone with N-acyl-2-aminothiazole at the C3 and C2 positions, yielding an α-glucosidase inhibitor, has also been previously described. Therefore, 3β-hydroxynootkatone has great potential for further research and for synthesizing new derivatives with valuable biological activities for agricultural and medicinal applications.

Harnessing bacterial metabolites for enhanced cancer chemotherapy: unveiling unique therapeutic potentials

Cancer poses a serious threat to health globally, with millions diagnosed every year. According to Global Cancer Statistics 2024, about 20 million new cases were reported in 2022, and 9.7 million people worldwide died of this condition. Advanced therapies include combination of one or more treatment procedures, depending on the type, stage, and particular genetic constitution of the cancer, which may include surgery, radiotherapy, chemotherapy, immunotherapy, hormone therapy, targeted therapy, and stem cell transplant. Also, awareness about lifestyle changes, preventive measures and screening at early stages has reduced the incidence of the disease; still, there is a major failure in controlling the incidence of cancer because of its complex and multifaceted nature. With increasing interest in bacterial metabolites as possible novel and effective treatment options in cancer therapy, their main benefits include not only direct anticancer effects but also the modulation of the immune system and potential for targeted and combination therapies. They can therefore be used in combination with chemotherapy, radiotherapy, or immunotherapy to improve outcomes or reduce side effects. Furthermore, nanoparticle-based delivery systems have the potential to enhance the potency and safety of anticancer drugs by providing improved stability, targeted release, and controlled delivery.

Alligamycin A, an antifungal β-lactone spiroketal macrolide from Streptomyces iranensis

Fungal infections pose a great threat to public health and there are only four main types of antifungal drugs, which are often limited with toxicity, drug-drug interactions and antibiotic resistance. Streptomyces is an important source of antibiotics, represented by the clinical drug amphotericin B. Here we report the discovery of alligamycin A (1) as an antifungal compound from the rapamycin-producer Streptomyces iranensis through genome-mining, genetics and natural product chemistry approaches. Alligamycin A harbors a unique chemical scaffold with 13 chiral centers, featuring a β-lactone moiety, a [6,6]-spiroketal ring, and an unreported 7-oxo-octylmalonyl-CoA extender unit incorporated by a potential crotonyl-CoA carboxylase/reductase. It is biosynthesized by a type I polyketide synthase which is confirmed through CRISPR-based gene editing. Alligamycin A displayed potent antifungal effects against numerous clinically relevant filamentous fungi, including resistant Aspergillus and Talaromyces species. β-Lactone ring is essential for the antifungal activity since alligamycin B (2) with disruption in the ring abolished the antifungal effect. Proteomics analysis revealed alligamycin A potentially disrupts the integrity of fungal cell walls and induces the expression of stress-response proteins in Aspergillus niger. Discovery of the potent antifungal candidate alligamycin A expands the limited antifungal chemical space.

Albusamides A-G: Hydroxylated Fatty Amine Derivatives from the Deep-Sea-Derived Actinomycete Streptomyces albus 228DD-066 and Their Cytotoxic Activity

A series of new hydroxylated fatty amine derivatives, albusamides A-G (1-7), along with four known compounds (8-11), which are reported for the first time from a natural source, were isolated from the culture broth of Streptomyces albus 228DD-066 derived from a deep-sea sediment sample gathered off the coast of Dokdo Island, Republic of Korea. Their structures were elucidated through the comprehensive analysis of 1D and 2D NMR spectra and HRESIMS, and absolute configurations were determined using the modified Mosher's method. Biological evaluations against solid and blood cancer cell lines revealed that these new metabolites have moderate to strong cytotoxic activity. Compound 3 exhibited high cytotoxic activity with GI50 values ranging from 0.4 to 0.6 μM against solid cancer cell lines and exhibited the strongest cytotoxicity (GI50 value = 0.2 μM) against the WSU-DLCL2 blood cancer cell line.

The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil

Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.

The HOMO-LUMO Gap as Discriminator of Biotic from Abiotic Chemistries

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (-10.4 ± 0.9 eV versus -12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The "hydrophilic reactivity" quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference.

Streptomyces fradiae Mitigates the Impact of Potato Virus Y by Inducing Systemic Resistance in Two Egyptian Potato (Solanum tuberosum L.) Cultivars

In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95-98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection.

Metabolomics Approach to Explore Bioactive Natural Products Derived From Plant-Root-Associated Streptomyces

Streptomyces, a prominent genus within the Actinomycetota phylum, is responsible for over 60% of clinically relevant antibiotics. Streptomyces strains inhabiting plant roots possess the potential to synthesize bioactive natural products, conferring defense and resilience to plants against pathogenic microorganisms. However, this potential remains largely unexplored. This study aims to screen for bioactive metabolites produced by Streptomyces strains in the plant rhizosphere.Six Streptomyces isolates were cultivated using three modified media to induce the production of diverse metabolites, employing the One Strain Many Compounds (OSMAC) approach. The metabolites present in extracts from fermentation broths were examined through a non-targeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) approach coupled with Global Natural Products Social Molecular Networking (GNPS MN). The antimicrobial activity of the extracts was assessed using the disc diffusion method.The strains demonstrated a wide-ranging antimicrobial efficacy against all examined organisms. The GNPS molecular network analyses reveal that metabolite profiles in extracts can exhibit variations based on the medium and solvent system employed. Notably, the ethyl acetate and dichloromethane extracts from Streptomyces sp. CAH29, cultivated in Glucose-Yeast Extract Medium (GYM), exhibited inhibition diameters of up to 30 mm against both Staphylococcus aureus and Candida albicans. Within the metabolomes of these strains, the antibiotics spiramycin and actinomycin were detected. Additionally, lyngbatoxin, a tumor promoter, and potential new analogs were identified. Significantly, a considerable portion of the produced metabolites did not align with any known compounds, indicating the existence of unidentified metabolites generated by these strains. This suggests the possibility of introducing novel chemical entities.Our study illustrated that Streptomyces strains associated with plant roots could be considered a valuable source of bioactive secondary metabolites. Furthermore, the metabolomics approach utilized in this study serves as a rapid and valuable tool for the screening of microorganisms capable of producing bioactive metabolites.

Discovery of two new actinobacteria, Micromonospora palythoicola sp. nov. and Streptomyces poriticola sp. nov., isolated from marine invertebrates

Marine invertebrates represent an underexplored reservoir for actinobacteria, which are known to synthesize novel bioactive compounds. This study isolated 37 actinobacterial strains from five distinct marine invertebrate hosts, namely Chondrilla australiensis, Palythoa sp., Favia sp., Porites lutea, and Acropora cervicornis, while no strains were obtained from Lissoclinum sp. and Lithophyllon sp. These isolates were taxonomically classified into six genera: Gordonia, Microbacterium, Micromonospora, Nocardia, Rhodococcus, and Streptomyces, with Streptomyces and Micromonospora being notably predominant. Comparative genomic analysis facilitated the identification of two novel species: Micromonospora palythoicola sp. nov. (strain S2-005T = TBRC 18343T and NBRC 116545T) and Streptomyces poriticola sp. nov. (strain C6-003T, =TBRC 17807T and NBRC 116425T). Both species exhibited substantial genetic differences from their nearest known species as demonstrated by digital DNA-DNA hybridization and average nucleotide identity scores, which fell below the thresholds of 70% and 95%, respectively. Streptomyces poriticola C6-003T displayed significant antimicrobial activity and selective cytotoxicity against human breast cancer MCF-7 cells, with reduced toxicity towards human dermal papilla cells. Micromonospora palythoicola S2-005T manifested antimicrobial properties against Streptococcus mutans and Kocuria rhizophila. These findings highlight the considerable diversity of actinobacteria within marine invertebrates and underscore their potential as a source of new species with promising biological properties for therapeutic applications.

Natural products with γ-pyrone scaffold from Streptomyces

The Streptomyces sp. is considered the vast reservoir of bioactive natural products belonging to different classes like polyketides, terpenoids, lanthipeptides, and non-ribosomal peptides to name a few. The ubiquitous distribution of the genus makes them capable of producing distinct compounds. Many of those compounds contain a unique γ-pyrone with various chemical structures and exhibit different bioactivities. One such class, nitrophenyl-γ-pyrone, constitutes different bioactive compounds isolated from Streptomyces sp. from different sources ranging from soil to marine environments. In addition, such compounds have antinematodal, cytotoxicity activities, and inhibition of adipogenesis. These compounds include aureothin (3), spectinabilin (7), and their derivatives. Moreover, there are other compounds like actinopyrones (11-16), benwamycins (22-23), and peucemycin and its derivatives (24-26) that also have antibacterial and anticancer activities. The other group classified as anthra-γ-pyrone has various bioactive natural products. For instance, tetrahydroanthra-γ-pyrone, shellmycin A-D (27-30) possess antibacterial as well as anticancer activities. In addition, the pluramycin family compounds belonging to anthra-γ-pyrone group also possess cytotoxic activity, for instance, kidamycin (31), rubiflavin, and their derivatives (33-37). Xanthones are another important group of natural products that also contain γ-pyrone ring producing different bioactivities. Albofungin (42) and its derivatives (43-46) belong to subgroup polycyclic tetrahydro xanthones that possess antibacterial, anticancer, and antibiofilm, antimacrofouling activities. Similarly, other compounds, belonging to this subgroup, exhibit different bioactivities like antifungal, antimalarial, and antibacterial activities and block transient receptor potential vanilloid 1 (TRPV1). These compounds include cervinomycins (48-55), citreamycins (56-57), sattahipmycin (59), and chrexanthomycins (60-63). This review gives succinct information on the γ-pyrone containing natural products isolated from Streptomyces sp. focusing on their structure and bioactivities. KEY POINTS: • The Streptomyces sp. is the producer of various bioactive natural products including the one with γ-pyrone ring. • These γ-pyrone compounds are structurally different and possess different bioactivities. • The Streptomyces has the potential to produce such compounds and the reservoir of these compounds is expected to increase in the future.

Biological characteristics of marine Streptomyces SK3 and optimization of cultivation conditions for production of compounds against Vibiriosis pathogen isolated from cultured white shrimp (Litopenaeus vannamei)

Antibiotic resistance in shrimp farms has emerged as an extremely serious situation worldwide. The main aim of this study was to optimize the cultural conditions for producing new antibiotic agents from marine Streptomyces species. Streptomyces SK3 was isolated from marine sediment and was identified by its 16S rDNA as well as biochemical characteristics. This microbe produced the highest concentration of bioactive secondary metabolites (BSMs) when cultured in YM medium (YM/2). It produced the maximum total protein (41.8 ± 6.36 mg/ml) during the late lag phase period. The optimum incubation temperature was recorded at 30 °C; BSMs were not produced at ≤10 °C within an incubation period of 3-4 days. The suitable agitation speed was found to be 200 rpm with pH 7.00. The proper carbon, nitrogen, and trace elements supplementation consisted of starch, malt extract, calcium carbonate (CaCO3), and magnesium sulfate (MgSO4). The ethyl acetate extract was found to act strongly against three vibriosis pathogens, Vibrio harveyi, Vibrio parahaemolyticus, and Vibrio vunificus, as indicated by the inhibition zones at 34.5, 35.4, and 34.3 mm, respectively. The extract showed the strongest anti-V. harveyi activity, as indicated by minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 0.101 ± 0.02 and 0.610 ± 0.04 mg/ml, respectively. Basic chemical investigation of the crude extract using thin layer chromatography (TLC), bioautography, liquid chromatography tandem mass spectrometry (LC‒MS/MS), Fourier transform infrared spectroscopy (FTIR), and proton nuclear magnetic resonance (1H-NMR) revealed that the active components were the terpenoid and steroid groups of compounds. They showed carboxylic acid and ester functions in their molecules.

Genomic Investigation of a Rhizosphere Isolate, Streptomyces sp. JL1001, Associated with Polygonatum cyrtonema Hua

In the present study, using genome mining, Streptomyces sp. JL1001, which possesses a leinamycin-type gene cluster, was identified from 14 strains of Streptomyces originating from the rhizosphere soil of Polygonatum cyrtonema Hua. The complete genome of Streptomyces sp. JL1001 was sequenced and analyzed. The genome of Streptomyces sp. JL1001 consists of a 7,943,495 bp chromosome with a 71.71% G+C content and 7315 protein-coding genes. We also identified 36 biosynthetic gene clusters (BGCs) for secondary metabolites in Streptomyces sp. JL1001. Twenty-seven BGCs had low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. In addition, a comparative analysis was conducted between the leinamycin-type gene cluster in Streptomyces sp. JL1001 and the biosynthetic gene clusters of leinamycin and largimycin. This study aims to provide a comprehensive analysis of the genomic features of rhizosphere Streptomyces sp. JL1001. It establishes the foundation for further investigation into experimental trials involving novel bioactive metabolites such as AT-less type I polyketides that have important potential applications in medicine and agriculture.

Functionalization of silk with actinomycins from Streptomyces anulatus BV365 for biomedical applications

Silk, traditionally acclaimed as the "queen of fiber," has been widely used thanks to its brilliant performance such as gentleness, smoothness and comfortableness. Owing to its mechanical characteristics and biocompatibility silk has a definitive role in biomedical applications, both as fibroin and fabric. In this work, the simultaneous dyeing and functionalization of silk fabric with pigments from Streptomyces anulatus BV365 were investigated. This strain produced high amounts of orange extracellular pigments on mannitol-soy flour agar, identified as actinomycin D, C2 and C3. The application of purified actinomycins in the dyeing of multifiber fabric was assessed. Actinomycins exhibited a high affinity towards protein fibers (silk and wool), but washing durability was maintained only with silk. Acidic condition (pH5) and high temperature (65°C) facilitated the silk dyeing. The morphologies and chemical components of the treated silk fabrics were analyzed using scanning electron microscopy and Fourier transform infrared spectroscopy. The results showed the pigments bind to the silk through interaction with the carbonyl group in silk fibroin rendering the functionalized, yet surface that does not cause skin irritation. The treated silk exhibited a remarkable antibacterial effect, while the biocompatibility test performed with 3D-reconstructed human epidermis model indicated safe biological properties, paving the way for future application of this material in medicine.

Bioactive Insecticides from Chemometric Diverse Ant-Associated Symbionts Streptomyces novaecaesareae and Streptomyces nojiriensis against the Fall Armyworm Larvae

The Streptomyces genus has long been recognized as a prolific and valuable source of diverse secondary metabolites. These metabolites contribute significantly to the intricate chemical diversity exhibited by Streptomyces, making them an indispensable reservoir for drug discovery, agricultural applications, and industrial processes. Exploiting the potential of these natural compounds holds the promise of ushering in a new era in insect pest management, reducing reliance on synthetic chemicals and fostering ecologically sustainable solutions. This study dives into the realm of chemo diversity within isolates of Streptomyces nojiriensis and Streptomyces novaecaesareae, with a specific focus on the production of insecticidal compounds. We explored chromatographic techniques for the identification and isolation of insecticidal compounds, and two bioactive compounds were identified in extracts of S. novaecaesareae. Valinomycin was identified from hexanic extracts of strain Asp59, while naphthomycin from ethyl acetate extracts of strain Asp58. These compounds showed insecticidal activity against first instars of Spodoptera frugiperda (Asp59: LC50 = 10.82 µg/µL, LC90 = 26.25 µg/µL; Asp58: LC50 = 15.05 µg/µL, LC90 = 38.84 µg/µL). Notably, this is the first report of naphthomycin as an insecticidal compound. The present study suggests that valinomycin and naphthomycin may be a novel biological source for the control of Spodoptera frugiperda in early stages.

Expanding the Phage Galaxy: Isolation and Characterization of Five Novel Streptomyces Siphoviruses Ankus, Byblos, DekoNeimoidia, Mandalore, and Naboo

Background

Key features of the actinobacterial genus Streptomyces are multicellular, filamentous growth, and production of a broad portfolio of bioactive molecules. These characteristics appear to play an important role in phage-host interactions and are modulated by phages during infection. To accelerate research of such interactions and the investigation of novel immune systems in multicellular bacteria, phage isolation, sequencing, and characterization are needed. This is a prerequisite for establishing systematic collections that appropriately cover phage diversity for comparative analyses.

Material & Methods

As part of a public outreach program within the priority program SPP 2330, involving local schools, we describe the isolation and characterization of five novel Streptomyces siphoviruses infecting S. griseus, S. venezuelae, and S. olivaceus.

Results

All isolates are virulent members of two existing genera and, additionally, establish a new genus in the Stanwilliamsviridae family. In addition to an extensive set of tRNAs and proteins involved in phage replication, about 80% of phage genes encode hypothetical proteins, underlining the yet underexplored phage diversity and genomic dark matter still found in bacteriophages infecting actinobacteria.

Conclusions

Taken together, phages Ankus, Byblos, DekoNeimoidia, Mandalore, and Naboo expand the phage diversity and contribute to ongoing research in the field of Streptomyces phage-host interactions.

Antarctic Streptomyces: Promising biocontrol agents for combating Fusarium oxysporum f. sp. cubense

Fusarium wilt of Banana (FWB) caused by Fusarium oxysporum f. sp. cubense (Foc) poses a significant threat to the banana industry, with current inadequate control measures. This study evaluated the antifungal potential of nine Streptomyces strains isolated from Antarctic soil samples, using Casein-Starch media to stimulate the production of antifungal compounds. The inhibition spectrum against Foc was assessed under laboratory conditions using the well diffusion on Mueller-Hinton agar, with antifungal activity measured in arbitrary units (AU/mL) and minimum inhibitory concentration (MIC) tested using ethyl acetate extracts. Among the nine isolates, K6 and E7 were closely related to Streptomyces polyrhachis and Streptomyces fildesensis, exhibited significant antifungal activity, with K6 and E7 showing 320 and 80 AU/mL, and MIC values of 250 and >500 ppm, respectively. These findings highlight K6 and E7 as potential biocontrol agents against Foc, offering new avenues for sustainable Fusarium wilt management in banana cultivation.

Unlocking the therapeutic potential of bioactive exopolysaccharide produced by marine actinobacterium Streptomyces vinaceusdrappus AMG31: A novel approach to drug development

Acidic exopolysaccharide (EPS) was produced by a marine actinobacterium Streptomyces vinaceusdrappus strain AMG31 with the highest yield of 10.6 g/l. The synthesized EPS has an average molecular weight of 5.1 × 104 g/mol and contains arabinose, glucose, galacturonic acid (0.5:2:2 M ratio), with 39.77 % uronic acid residues and 18.8 % sulfate detected. EPS exhibited antioxidant activities with 93.8 % DPPH radical scavenging and 344.7 μg/mg total antioxidant capacity. It displayed anti-inflammatory effects by inhibiting 5-LOX and COX-2. Regarding the cytotoxic activity, the IC50 values are 301.6 ± 11.8, 260.8 ± 12.2, 29.4 ± 13.5, 351.3 ± 11.2, 254.1 ± 9.8, and 266.5 ± 10.4 μg/ml for PC-3, HEP-2, MCF-7, HCT-116, A-549, HepG-2 respectively, which indicate that the produced EPS does not have strong cytotoxic activities. Moreover, the EPS showed anti-Alzheimer activity via inhibition of the Butyrylcholinesterase enzyme, with the highest percentage of 84.5 % at 100 μg/ml. Interestingly, the EPS showed superior anti-obesity activity by inhibiting lipase enzyme with a rate of 95.3 % compared to orlistat as a positive control (96.8 %) at a concentration of 1000 μg/ml. Additionally, the produced EPS displayed the highest anti-diabetic properties by inhibiting α-amylase (IC50 31.49 μg/ml) and α-glucosidase (IC50 6.48 μg/ml), suggesting antidiabetic potential analogous to acarbose. EPS exhibited promising antibacterial and antibiofilm activity against a wide range of Gram-positive and Gram-negative pathogenic bacteria.

Bioactive Streptomycetes: A Powerful Tool to Synthesize Diverse Nanoparticles With Multifarious Properties

Nanobiotechnology has gained significant attention due to its capacity to generate substantial benefits through the integration of microbial biotechnology and nanotechnology. Among microbial organisms, Actinomycetes, particularly the prominent genus Streptomycetes, have garnered attention for their prolific production of antibiotics. Streptomycetes have emerged as pivotal contributors to the discovery of a substantial number of antibiotics and play a dominant role in combating infectious diseases on a global scale. Despite the noteworthy progress achieved through the development and utilization of antibiotics to combat infectious pathogens, the prevalence of infectious diseases remains a prominent cause of mortality worldwide, particularly among the elderly and children. The emergence of antibiotic resistance among pathogens has diminished the efficacy of antibiotics in recent decades. Nevertheless, Streptomycetes continue to demonstrate their potential by producing bioactive metabolites for the synthesis of nanoparticles. Streptomycetes are instrumental in producing nanoparticles with diverse bioactive characteristics, including antiviral, antibacterial, antifungal, antioxidant, and antitumor properties. Biologically synthesized nanoparticles have exhibited a meaningful reduction in the impact of antibiotic resistance, providing resources for the development of new and effective drugs. This review succinctly outlines the significant applications of Streptomycetes as a crucial element in nanoparticle synthesis, showcasing their potential for diverse and enhanced beneficial applications.

Cytotoxic glutarimide-containing polyketides isolated from Streptomyces sp. JCM 4793

Glutarimide-containing polyketides usually exhibit anti-fungi activity, which was well exampled by cycloheximide. In our work, three new polyketide structures, 12-amidestreptimidone (1), 12-carboxylstreptimidone (2) and 3-(5S,8R)-(2-amino-2-oxoethyl-2'-methoxy-2'-oxoethyl)-8,10-dimethyl-7-oxododeca-5-hydroxy-9E,11-diolefin (3) were isolated from Streptomyces sp. JCM 4793. 3 without the glutarimide moiety is not active against fungi as expected, while 1 bearing the amide moiety is much more active than its carboxylic form 2. Here we report the isolation, structural elucidation, antifungal activity, and proposed biosynthesis pathway of 1-3.

Whole genome-based comparative analysis of the genus Streptomyces reveals many misclassifications

Streptomyces species are experts in the production of bioactive secondary metabolites; however, their taxonomy has fallen victim of the tremendous interest shown by the scientific community, evident in the discovery of numerous synonymous in public repositories. Based on genomic data from NCBI Datasets and nomenclature from the LPSN database, we compiled a dataset of 600 Streptomyces species along with their annotations and metadata. To pinpoint the most suitable taxonomic classification method, we conducted a comprehensive assessment comparing multiple methodologies, including analysis of 16S rRNA, individual housekeeping genes, multilocus sequence analysis (MLSA), and Fast Average Nucleotide Identity (FastANI) on a subset of 409 species with complete data. Due to insufficient resolution of 16S rRNA and inconsistency observed in individual housekeeping genes, we performed a more in-depth analysis, comparing only FastANI and MLSA, which expanded our dataset to include 502 species. With FastANI validated as the preferred method, we conducted pairwise analysis on the entire dataset identifying 59 non-unique species among the 600, and subsequently refined the dataset to 541 unique species. Additionally, we collected data on 724 uncharacterized Streptomyces strains to investigate the uniqueness potential of the unannotated fraction of the Streptomyces genus. Utilizing FastANI, 289 strains could be successfully classified into one of the 541 Streptomyces species. KEY POINTS: • Evaluation of taxonomic classification methods for Streptomyces species. • Whole genome analysis, specifically FastANI, has been chosen as preferred method. • Various reclassifications are proposed within the Streptomyces genus.

A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation

Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.

Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in Streptomyces bacteria

Ribosomally synthesized post-translationally modified peptides (RiPPs) are a novel category of bioactive natural products (NPs). Streptomyces bacteria are a potential source of many bioactive NPs. Limited opportunities are available to characterize all the bioactive NP gene clusters. In this study, 410 sequences of Streptomyces were analyzed for RiPPs through genome mining using the National Center for Biotechnology Information (NCBI), by combining BAGEL and anti-SMASH. A total of 4098 RiPPs were found; including both classified (lanthipeptide, RiPP-like, bacteriocin, LAPs, lassopeptide, thiopeptides) and nonclassified RiPPs. Soil was identified as a rich habitat for RiPPs. These data may offer alternative future remedies for various health issues.

Role of Carbon, Nitrogen, Phosphate and Sulfur Metabolism in Secondary Metabolism Precursor Supply in Streptomyces spp

The natural soil environment of Streptomyces is characterized by variations in the availability of nitrogen, carbon, phosphate and sulfur, leading to complex primary and secondary metabolisms. Their remarkable ability to adapt to fluctuating nutrient conditions is possible through the utilization of a large amount of substrates by diverse intracellular and extracellular enzymes. Thus, Streptomyces fulfill an important ecological role in soil environments, metabolizing the remains of other organisms. In order to survive under changing conditions in their natural habitats, they have the possibility to fall back on specialized enzymes to utilize diverse nutrients and supply compounds from primary metabolism as precursors for secondary metabolite production. We aimed to summarize the knowledge on the C-, N-, P- and S-metabolisms in the genus Streptomyces as a source of building blocks for the production of antibiotics and other relevant compounds.

Oligomycin-producing Streptomyces sp. newly isolated from Swiss soils efficiently protect Arabidopsis thaliana against Botrytis cinerea

Botrytis cinerea is a necrotrophic phytopathogen able to attack more than 200 different plant species causing strong yield losses worldwide. Many synthetic fungicides have been developed to control this disease, resulting in the rise of fungicide-resistance B. cinerea strains. The aim of this study was to identify Streptomyces strains showing antagonistic activity against B. cinerea to contribute to plant protection in an environmentally friendly way. We isolated 15 Actinomycete strains from 9 different Swiss soils. The culture filtrates of three isolates showing antifungal activity inhibited spore germination and delayed mycelial growth of B. cinerea. Infection experiments showed that Arabidopsis thaliana plants were more resistant to this pathogen after leaf treatment with the Streptomyces filtrates. Bioassay-guided isolation of the active compounds revealed the presence of germicidins A and B as well as of oligomycins A, B, and E. While germicidins were mostly inactive, oligomycin B reduced the mycelial growth of B. cinerea significantly. Moreover, all three oligomycins inhibited this fungus' spore germination, suggesting that these molecules might contribute to the Streptomyces's ability to protect plants against infection by the broad host-pathogen Botrytis cinerea.

IMPORTANCE

This study reports the isolation of new Streptomyces strains with strong plant-protective potential mediated by their production of specialized metabolites. Using the broad host range pathogenic fungus Botrytis cinerea, we demonstrate that the cell-free filtrate of selected Streptomyces isolates efficiently inhibits different developmental stages of the fungus, including mycelial growth and the epidemiologically relevant spore germination. Beyond in vitro experiments, the strains and their metabolites also efficiently protected plants against the disease caused by this pathogen. This work further identifies oligomycins as active compounds involved in the observed antifungal activity of the strains. This work shows that we can harness the natural ability of soil-borne microbes and of their metabolites to efficiently fight other microbes responsible for significant crop losses. This opens the way to the development of environmentally friendly health protection measures for crops of agronomical relevance, based on these newly isolated strains or their metabolic extracts containing oligomycins.

Deletions of conserved extracytoplasmic function sigma factors-encoding genes in Streptomyces have a major impact on secondary metabolism

BACKGROUND

Ethanol shock significantly affects expression of over 1200 genes in Streptomyces venezuelae NRRL B-65,442, including those involved in secondary metabolite biosynthesis and a cryptic gene pepX, which encodes a 19-amino acid peptide with an unknown function.

RESULTS

To establish a possible correlation between the PepX peptide and secondary metabolism in S. venezuelae, its gene was deleted, followed by analyses of the transcriptome and secondary metabolome of the mutant. Although the secondary metabolome of the pepX mutant was not strongly affected, pepX deletion, similar to ethanol shock, mostly resulted in downregulated expression of secondary metabolite biosynthesis gene clusters (BGCs). At the same time, there was a reverse correlation between the expression of certain extracytoplasmic function sigma factors (ECFs) and several BGCs. Individual deletions of three selected ECF-coding genes conserved in Streptomyces that were upregulated upon both pepX deletion and ethanol shock, had a profound positive effect on the expression of BGCs, which also correlated with the overproduction of specific secondary metabolites. Deletion of one such ECF-coding gene in a marine sponge-derived Streptomyces sp. also significantly altered the secondary metabolite profile, suggesting an important role of this ECF in the regulation of secondary metabolism.

CONCLUSIONS

These findings pave the way for the activation or upregulation of BGCs in Streptomyces bacteria harboring genes for ECFs homologous to those identified in this study, hereby assisting in the discovery of novel bioactive secondary metabolites.

Antibacterial activity and biosynthetic potential of Streptomyces sp. PBR19, isolated from forest rhizosphere soil of Assam

An Actinomycetia isolate, designated as PBR19, was derived from the rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate, identified as Streptomyces sp., shares a sequence similarity of 93.96% with its nearest type strain, Streptomyces atrovirens. This finding indicates the potential classification of PBR19 as a new taxon within the Actinomycetota phylum. PBR19 displayed notable antibacterial action against some ESKAPE pathogens. The ethyl acetate extract of PBR19 (EtAc-PBR19) showed the lowest minimum inhibitory concentration (MIC) of ≥ 0.195 µg/mL against Acinetobacter baumannii ATCC BAA-1705. A lower MIC indicates higher potency against the tested pathogen. Scanning electron microscope (SEM) findings revealed significant changes in the cytoplasmic membrane structure of the pathogen. This suggests that the antibacterial activity may be linked to the disruption of the microbial membrane. The predominant chemical compound detected in the EtAc-PBR19 was identified as phenol, 3,5-bis(1,1-dimethylethyl), comprising 48.59% of the area percentage. Additionally, PBR19 was found to contain the type II polyketide synthases (PKS type II) gene associated with antibiotic synthesis. The predicted gene product of PKSII was identified as the macrolide antibiotic Megalomicin A. The taxonomic distinctiveness, potent antibacterial effects, and the presence of a gene associated with antibiotic synthesis suggest that PBR19 could be a valuable candidate for further exploration in drug development and synthetic biology. The study contributes to the broader understanding of microbial diversity and the potential for discovering bioactive compounds in less-explored environments.

Genetic Diversity of Ralstonia solanacearum Causing Tobacco Bacterial Wilt in Fujian Province and Identification of Biocontrol Streptomyces sp

Tobacco bacterial wilt is a highly destructive soilborne disease caused by the Ralstonia solanacearum species complex, exhibiting a significant risk to global flue-cured tobacco cultivation and resulting in substantial economic loss. In this study, 77 isolates were collected from three prominent flue-cured tobacco cultivation areas in Fujian, China (Nanping, Sanming, and Longyan), in 2021 and 2022. The isolated strains were classified through phylotype-specific multiplex polymerase chain reaction (Pmx-PCR) and physiological tests. The analysis showed that all the strains were associated with phylotype I, race 1, and biovar III. Subsequent phylogenetic analysis using partial egl gene sequences classified the 77 isolates into 5 distinct sequevars: 13, 15, 16, 17, and 34. Notably, a remarkable predominance of sequevar 15 was observed in Fujian Province, while sequevar 16 was first reported on tobacco in China, which was identified in other plants, expanding the understanding of its host range and distribution in the country. In addition, a Streptomyces strain extracted from the rhizosphere soil of tobacco was found to inhibit the growth of multiple sequevars of tobacco R. solanacearum, indicating its broad-spectrum antagonistic properties. Furthermore, pot experiments showed that the strain St35 effectively controlled tobacco bacterial wilt. The isolate St35 was conclusively identified as Streptomyces gancidicus according to the morphological and genetic features. In summary, the present study demonstrated the genetic diversity and distribution of tobacco R. solanacearum strains in the Fujian province of China, as well as the identification of a candidate biological control agent for the management of tobacco bacterial wilt.

Potential of Streptomyces avermitilis: A Review on Avermectin Production and Its Biocidal Effect

Secondary metabolites produced by the fermentation of Streptomyces avermitilis bacterium are powerful antiparasitic agents used in animal health, agriculture and human infection treatments. Avermectin is a macrocyclic lactone with four structural components (A1, A2, B1, B2), each of them containing a major and a minor subcomponent, out of which avermectin B1a is the most effective parasitic control compound. Avermectin B1a produces two homologue avermectins (B1 and B2) that have been used in agriculture as pesticides and antiparasitic agents, since 1985. It has a great affinity with the Cl-channels of the glutamate receptor, allowing the constant flow of Cl- ions into the nerve cells, causing a phenomenon of hyperpolarization causing death by flaccid paralysis. The purpose of this work was to gather information on the production of avermectins and their biocidal effects, with special emphasis on their role in the control of pests and phytopathogenic diseases. The literature showed that S. avermitilis is an important producer of macrocyclic lactones with biocidal properties. In addition, avermectin contributes to the control of ectoparasites and endoparasites in human health care, veterinary medicine and agriculture. Importantly, avermectin is a compound that is harmless to the host (no side effects), non-target organisms and the environment.

Streptomyces-Fungus Co-Culture Enhances the Production of Borrelidin and Analogs: A Genomic and Metabolomic Approach

The marine Streptomyces harbor numerous biosynthetic gene clusters (BGCs) with exploitable potential. However, many secondary metabolites cannot be produced under laboratory conditions. Co-culture strategies of marine microorganisms have yielded novel natural products with diverse biological activities. In this study, we explored the metabolic profiles of co-cultures involving Streptomyces sp. 2-85 and Cladosporium sp. 3-22-derived from marine sponges. Combining Global Natural Products Social (GNPS) Molecular Networking analysis with natural product database mining, 35 potential antimicrobial metabolites annotated were detected, 19 of which were exclusive to the co-culture, with a significant increase in production. Notably, the Streptomyces-Fungus interaction led to the increased production of borrelidin and the discovery of several analogs via molecular networking. In this study, borrelidin was first applied to combat Saprolegnia parasitica, which caused saprolegniosis in aquaculture. We noted its superior inhibitory effects on mycelial growth with an EC50 of 0.004 mg/mL and on spore germination with an EC50 of 0.005 mg/mL compared to the commercial fungicide, preliminarily identifying threonyl-tRNA synthetase as its target. Further analysis of the associated gene clusters revealed an incomplete synthesis pathway with missing malonyl-CoA units for condensation within this strain, hinting at the presence of potential compensatory pathways. In conclusion, our findings shed light on the metabolic changes of marine Streptomyces and fungi in co-culture, propose the potential of borrelidin in the control of aquatic diseases, and present new prospects for antifungal applications.

The Co-Inoculation Effect on Triticum aestivum Growth with Synthetic Microbial Communities (SynComs) and Their Potential in Agrobiotechnology

The use of rhizospheric SynComs can be a new and sustainable strategy in the agrobiotechnology sector. The objective of this study was to create the most appropriate SynCom composition; examine the ability to dissolve natural rock phosphate (RP) from Morocco in liquid-modified NBRIP medium; determine organic acids, and phytohormones; and verify plant growth promoting and nutrition uptake effect in the pot experiments of winter wheat (Triticum aestivum). A total of nine different microorganisms were isolated, which belonged to three different genera: Bacillus, Pseudomonas, and Streptomyces. Out of the 21 treatments tested, four SynComs had the best phosphate-dissolving properties: IJAK-27+44+91 (129.17 mg L-1), IIBEI-32+40 (90.95 µg mL-1), IIIDEG-45+41 (122.78 mg L-1), and IIIDEG-45+41+72 (120.78 mg L-1). We demonstrate that these SynComs are capable of producing lactic, acetic, gluconic, malic, oxalic, citric acids, and phytohormones such as indole-3-acetic acid, zeatin, gibberellic acid, and abscisic acid. In pot experiments with winter wheat, we also demonstrated that the designed SynComs were able to effectively colonize the plant root rhizosphere and contributed to more abundant plant growth characteristics and nutrient uptake as uninoculated treatment or uninoculated treatment with superphosphate (NPK 0-19-0). The obtained results show that the SynCom compositions of IJAK-27+44+91, IIBEI-32+40, IIIDEG-45+41, and IIIDEG-45+41+72 can be considered as promising candidates for developing biofertilizers to facilitate P absorption and increase plant nutrition.

Streptomyces use umbrella toxins to gently compete with kin

In a recent issue of Nature, Zhao et al. have demonstrated that Streptomyces spp. produce "umbrella"-shaped polymorphic toxin particles, a novel class of non-lethal toxins that gently inhibit competitors by arresting hyphal growth in closely related bacteria, unveiling a unique bacterial defense strategy in microbial ecological interactions.1.

Characterization and antibacterial evaluation of Eco-friendly silver nanoparticles synthesized by halophilic Streptomyces rochei SSCM102 isolated from mangrove sediment

BACKGROUND

Antimicrobial resistance has surged due to widespread antimicrobial drug use, prompting interest in biosynthesizing nanoparticles from marine-derived actinomycetes extracellular metabolites, valued for their diverse bioactive compounds. This approach holds promise for addressing the urgent need for novel antimicrobial agents. The current study aimed to characterize novel bioactive compounds from unexplored biodiversity hotspots, halophilic Streptomyces sp. isolated from mangrove sediment in the Pichavaram region, India.

METHODS AND RESULTS

Streptomyces rochei SSCM102 was conclusively identified through morphological and molecular characterization. Synthesis of silver nanoparticles (AgNPs) from Streptomyces rochei SSCM102 was characterized using various techniques, including UV-Vis, XRD, SEM, EDX, and FT-IR. The UV-Vis spectrum of the reduced AgNPs exhibited a prominent peak at 380 nm, confirming the AgNPs. The UV-Vis spectrum confirmed the synthesis of AgNP, and SEM analysis revealed a cubic morphology with sizes ranging from 11 to 21 nm. The FTIR spectrum demonstrated a shift in frequency widths between 626 cm-1 and 3432 cm-1. The EDX analysis substantiated the presence of metallic silver, evident from a strong band at 1.44 keV. The synthesized AgNPs exhibited antibacterial efficacy against human pathogens Escherichia coli (64 ± 0.32 µg/ml), Klebsiella pneumoniae (32 ± 0.16 µg/ml), and Pseudomonas aeruginosa (16 ± 0.08 µg/ml) by MIC and MBC values of 128 ± 0.64 (µg/ml), 64 ± 0.32 (µg/ml) and 32 ± 0.16 (µg/ml), respectively. Additionally, at a concentration of 400 µg/ml, the AgNPs displayed a 72% inhibition of DPPH radicals, indicating notable antioxidant capacity. The LC50 value of 130 µg/mL indicates that the green-synthesized AgNPs have lower toxicity by Brine Shrimp Larvae assay.

CONCLUSION

The study's novel approach to synthesizing eco-friendly silver nanoparticles using Halophilic Streptomyces rochei SSCM102 contributes significantly to the field of biomedical research and drug development. By demonstrating potent antibacterial properties and aligning with sustainability goals, these nanoparticles offer promising avenues for novel antibacterial therapies.

Exploring the Potential of Halotolerant Actinomycetes from Rann of Kutch, India: A Study on the Synthesis, Characterization, and Biomedical Applications of Silver Nanoparticles

A tremendous increase in the green synthesis of metallic nanoparticles has been noticed in the last decades, which is due to their unique properties at the nano dimension. The present research work deals with synthesis mediated by the actinomycete Streptomyces tendae of silver nanoparticles (AgNPs), isolated from Little and Greater Rann of Kutch, India. The confirmation of the formation of AgNPs by the actinomycetes was carried out by using a UV-Vis spectrophotometer where an absorbance peak was obtained at 420 nm. The X-ray diffraction pattern demonstrated five characteristic diffraction peaks indexed at the lattice plane (111), (200), (231), (222), and (220). Fourier transform infrared showed typical bands at 531 to 1635, 2111, and 3328 cm-1. Scanning electron microscopy shows that the spherical-shaped AgNPs particles have diameters in the range of 40 to 90 nm. The particle size analysis displayed the mean particle size of AgNPs in aqueous medium, which was about 55 nm (±27 nm), bearing a negative charge on their surfaces. The potential of the S. tendae-mediated synthesized AgNPs was evaluated for their antimicrobial, anti-methicillin-resistant Staphylococcus aureus (MRSA), anti-biofilm, and anti-oxidant activity. The maximum inhibitory effect was observed against Pseudomonas aeruginosa at (8 µg/mL), followed by Escherichia coli and Aspergillus niger at (32 µg/mL), and against Candida albicans (64 µg/mL), whereas Bacillus subtilis (128 µg/mL) and Staphylococcus aureus (256 µg/mL) were much less sensitive to AgNPs. The biosynthesized AgNPs displayed activity against MRSA, and the free radical scavenging activity was observed with an increase in the dosage of AgNPs from 25 to 200 µg/mL. AgNPs in combination with ampicillin displayed inhibition of the development of biofilm in Pseudomonas aeruginosa and Streptococcus pneumoniae at 98% and 83%, respectively. AgNPs were also successfully coated on the surface of cotton to prepare antimicrobial surgical cotton, which demonstrated inhibitory action against Bacillus subtilis (15 mm) and Escherichia coli (12 mm). The present research integrates microbiology, nanotechnology, and biomedical science to formulate environmentally friendly antimicrobial materials using halotolerant actinomycetes, evolving green nanotechnology in the biomedical field. Moreover, this study broadens the understanding of halotolerant actinomycetes and their potential and opens possibilities for formulating new antimicrobial products and therapies.

Genomic insights into an endophytic Streptomyces sp. VITGV156 for antimicrobial compounds

Endophytic Streptomyces sp. are recognized as a potential resource for valuable natural products but are less explored. This study focused on exploring endophytic Streptomyces species residing within tomato plants (Solanum lycopersicum) harboring genes for the production of a novel class of antibiotics. Our research involved the isolation and characterization of Streptomyces sp. VITGV156, a newly identified endophytic Streptomyces species that produces antimicrobial products. VITGV156 harbors a genome of 8.18 mb and codes 6,512 proteins, of which 4,993 are of known function (76.67%) and 1,519 are of unknown function (23.32%). By employing genomic analysis, we elucidate the genome landscape of this microbial strain and shed light on various BGCs responsible for producing polyketide antimicrobial compounds, with particular emphasis on the antibiotic kendomycin. We extended our study by evaluating the antibacterial properties of kendomycin. Overall, this study provides valuable insights into the genome of endophytic Streptomyces species, particularly Streptomyces sp. VITGV156, which are prolific producers of antimicrobial agents. These findings hold promise for further research and exploitation of pharmaceutical compounds, offering opportunities for the development of novel antimicrobial drugs.

Probiotic potential of a novel endophytic Streptomyces griseorubens CIBA-NS1 isolated from Salicornia sp. against Vibrio campbellii infection in shrimp

A novel endophytic Streptomyces griseorubens CIBA-NS1 was isolated from a salt marsh plant Salicornia sp. The antagonistic effect of S. griseorubens against Vibrio campbellii, was studied both in vitro and in vivo. The strain was validated for its endophytic nature and characterized through scanning electron microscopy, morphological and biochemical studies and 16SrDNA sequencing. The salinity tolerance experiment has shown that highest antibacterial activity was at 40‰ (16 ± 1.4 mm) and lowest was at 10 ‰ salinity (6.94 ± 0.51 mm). In vivo exclusion of Vibrio by S. griseorubens CIBA-NS1 was studied in Penaeus indicus post larvae and evaluated for its ability to improve growth and survival of P. indicus. After 20 days administration of S. griseorubens CIBA-NS1, shrimps were challenged with V. campbellii. The S. griseorubens CIBA-NS1 reduced Vibrio population in test group when compared to control, improved survival (60.5 ± 6.4%) and growth, as indicated by weight gain (1.8 ± 0.05g). In control group survival and growth were 48.4 ± 3.5% and 1.4 ± 0.03 g respectively. On challenge with V. campbellii, the S. griseorubens CIBA-NS1 administered group showed better survival (85.6 ± 10%) than positive control (64.3 ± 10%). The results suggested that S. griseorubens CIBA-NS1 is antagonistic to V. campbellii, reduce Vibrio population in the culture system and improve growth and survival. This is the first report on antagonistic activity of S. griseorubens isolated from salt marsh plant Salicornia sp, as a probiotic candidate to prevent V. campbellii infection in shrimps.