Search Results (171)

Allyl isothiocyanate (AITC) is effective as a bio-based fumigant in controlling soil-borne diseases; however, the selective pressure it exerts on soil microecology and evolutionary dynamics remains inadequately characterized. This study systematically investigated the remodeling effects of continuous AITC fumigation on soil microbial communities, functional genes, and functional strains by integrating metagenomic analysis and pure culture techniques. Results demonstrate that AITC drives directional selection from “sensitive” to “tolerant” microorganisms. Fungal communities exhibit greater cumulative damage than bacterial communities, with the proportion of significantly suppressed fungi increasing linearly from 9.3% at baseline to 35.7%. At the genus level, sensitive groups were predominantly enriched in pathogen-associated genera, e.g., Pseudomonas and Xanthomonas, whereas tolerant groups, represented by Bacillus and Streptomyces, maintained ecological dominance under continuous stress. Functionally, AITC induced differential evolution of functional gene repertoires. Nitrogen cycle genes (e.g., amoC) exhibited high negative sensitivity, with significant downregulation by 20%, whereas the TCA core module in the carbon cycle exhibited strong robustness. Virulence assays confirmed EC₅₀ values for tolerant beneficial bacteria (Bacillus spp.) (>40 mg·L⁻¹) were significantly higher than those for pathogens (1.3–7.9 mg/L). This study established a microbial “sensitive-tolerant” response framework under AITC stress, revealing the core potential of endogenous tolerant strains for the precise ecological restoration of fumigated soils. Full article

Streptomyces is a versatile genus widely used in drug production and biotechnological applications. This study aimed to identify and characterize bioactive compounds produced by Streptomyces UP-AC4 and UP-3.2 strains and evaluate their antibacterial and anticancer activities. The strains were identified as Streptomyces californicus and Streptomyces purpurascens via chemotaxonomy, 16S rRNA sequencing, amplified ribosomal DNA restriction analysis, and phylogenetic analysis. Bioactive compounds were extracted using heat treatments at 63 °C for 30 min or 73–110 °C for 10 min. Antibacterial activity against Staphylococcus aureus, Bacillus cereus, and Escherichia coli was assessed by agar disc assay, with MICs of 0.024–0.195 mg/mL and MBCs of 0.098–0.391 mg/mL for the most effective extracts. Anticancer activity against A549, H1299, and Lu99 lung cancer cells was evaluated using the MTT assay, showing IC₅₀ values of 0.23 ± 0.06 to 4.85 ± 0.64 mg/mL, while exhibiting no toxicity to normal fibroblast cells. HPLC analysis indicated that heat-assisted extraction of UP-AC4 at 73 °C for 10 min enriched a dinactin-associated compound as a predominant metabolite with antibiotic and anticancer activities. In conclusion, Streptomyces UP-AC4 and UP-3.2 produce promising low-cost bioactive compounds with strong potential for pharmaceutical and healthcare applications. Full article

Background. The genus Streptomyces is known for its capability to produce a wide range of bioactive secondary metabolites. The enzymes required for their synthesis are encoded within biosynthetic gene clusters (BGCs), whose expression can be influenced by various physical and nutritional factors. Among these nutritional factors, it is worth highlighting carbon catabolic repression (CCR), which prevents the formation of secondary metabolites. It has been shown that transcriptional factors, in turn, regulated by glucose or by the enzyme glucose kinase (Glk), may be involved in this mechanism. It was shown that the expression of some transcriptional factors is regulated by glucose availability and that the enzyme glucose kinase (Glk) may play a role in this process. One of the transcriptional factors most upregulated in the presence of glucose/agar in Streptomyces coelicolor M145 is SCO7424, a member of the MarR family of transcriptional regulators. However, its influence on antibiotic synthesis has never been studied. Objective. In this work, we evaluated the effect of SCO7424 overexpression on the synthesis of actinorhodin (ACT) and undecylprodigiosin (RED), and its impact on growth and glucose consumption. Methods. A copy of the sco7424 gene was cloned into the pIJ702 plasmid, which was then transformed into a wild-type strain of S. coelicolor M145. Growth and antibiotic production were evaluated in the strain with two copies of sco7424 and in the wild-type strain. We also evaluated the expression of the probable target genes by quantitative RT-PCR. Results. We found that overexpression of sco7424 negatively impacts growth, glucose consumption kinetics, and the expression of specific regulators of the ACT and RED biosynthetic pathways, resulting in reduced ACT and RED production. Understanding the function of the regulatory cascades regulated by this family of regulators is crucial for boosting the yields of valuable metabolites produced by industrial strains. Full article

The genus Streptomyces is the largest group within the phylum Actinobacteria, recognized for producing antibiotics and enzymes, with wide applications in medicine and biological control for crop protection against phytopathogens. In this study, the Streptomyces sp. Caat 5-35 strain, isolated from soil of the Caatinga biome in Brazil, and identified by analysis of the 16S rRNA gene, demonstrated its antagonistic effect in vitro in dual cultures against Phytophthora palmivora, Colletotrichum acutatum, Fusarium oxysporum, Rhizoctonia solani, Sclerotinia sclerotiorum, and Fusarium graminearum. Caat 5-35 inhibited mycelial growth ranging from 19% to 73.3%. Compounds purified by prep-HPLC from extracts were identified by spectral data analysis using UHPLC-triple-TOF-MS/MS, or nuclear magnetic resonance (NMR). This work demonstrated for the first time the anti-oomycete activity of albofungin, its derivatives, and albonoursin against P. palmivora. Moreover, the growth inhibition of Colletotrichum gloeosporioides by albonoursin and the antibacterial effect of 2-chloroadenosine and 5′-O-sulfamoyl-2-chloroadenosine against Pectobacterium carotovorum were demonstrated as novel findings. Caat 5-35 exhibited the ability to solubilize phosphates and produce cellulases on CMC agar. The findings of this study, in combination with in vitro bioassays on cacao pods (Theobroma cacao L.) inoculated with the antagonist strain and P. palmivora APB-35, demonstrate that Streptomyces sp. Caat 5-35 is a source of natural products with applications in agriculture and could serve as an alternative for crop protection. Full article

Postharvest diseases represent a critical challenge for global agriculture, resulting in substantial economic losses and threatening worldwide food security. Species of the genus Colletotrichum stand out among the main phytopathogens for being responsible for up to 40% of postharvest losses in various crops, including Capsicum species. This study evaluated the antifungal activity of two Streptomyces strains isolated from Amazonian sediments against different Colletotrichum species, with a focus on C. scovillei, the causal agent of anthracnose in Capsicum chinense fruits. Multilocus phylogenetic analyses indicated that strain APUR 32.5 possibly represents a new species, while MPUR 40.3 was identified as Streptomyces murinus. Both strains exhibited in vitro antifungal activity against seven Colletotrichum species, with inhibition percentages ranging from 56.3% to 88.6%. In fruit bioassays, S. murinus MPUR 40.3 reduced the incidence of anthracnose by 95%, while Streptomyces sp. APUR 32.5 achieved a 39.25% reduction. Scanning electron microscopy revealed complementary mechanisms of antifungal action, with MPUR 40.3 acting during the early infection stages through germination tube lysis, while APUR 32.5 targeted established mycelial structures through hyphal degradation. Additionally, both strains demonstrated plant growth-promoting capacity and exhibited biotechnologically relevant characteristics, including production of hydrolytic enzymes, siderophores, and phosphate solubilization ability. These results highlight the biotechnological promise of these Amazonian isolates as multifunctional agents for the sustainable management of anthracnose in Capsicum peppers. Full article

The presence of substantial amounts of heavy metals in the environment can result in various significant ecological issues and human health risks. Currently, bioremediation employing microorganisms is garnering significant interest due to its effectiveness. The present investigation aimed to isolate actinobacterial strains from an Italian mine and to characterise them for heavy metals resistance and plant growth-promoting characteristics. The different samples were processed for DNA extraction and 16S rRNA gene metabarcoding to investigate the bacteria and archaea communities. Cultivable microbiota were isolated and evaluated for heavy metals tolerance and different PGP traits. The most pertinent strains were tested for compatibility, merged into a consortium, and tested on Lemna minor L. Metabarcoding analysis revealed that amplicon sequence variants (ASVs) at the phylum level were mostly assigned to proteobacteria and bacteroidota. Uncultured and unknown taxa were the most prevalent in the samples at the genus level. A total of ten strains were obtained from the culture-dependent approach exhibiting interesting heavy metals tolerance and plant growth-promoting traits. The best strains (MTW 1 and MTW 5) were selected and further characterised by 16S barcoding. These strains were identified as Streptomyces atratus (99.57% identity). An in planta experiment showed that the metal-tolerant consortium MTW 1-5 improved plant physiology by significantly optimising plant growth and tolerance to heavy metals. The experiment conducted provided evidence for the possibility of using actinobacteria as bioaugmentation agents to improve the phytoextraction abilities of L. minor. Full article

Morels are a rare edible and medicinal fungus. A major factor contributing to difficulties with their continuous cropping is alteration in soil microbial communities. Pseudomonas putida is a key microorganism in morel cultivation soils; it has garnered significant attention due to its ability to degrade 1-aminocyclopropane-1-carboxylic acid (ACC), a precursor of ethylene. However, the interaction between Pseudomonas putida and morels remains unclear. This study evaluated the growth-promoting potential of P. putida KT2440 by measuring the casing soil ACC content and assessing its ACC utilization capacity. Metagenomic sequencing was performed to assess the changes in soil microbial composition and function. The results indicated that ACC accumulated in the soil following morel cultivation and that P. putida KT2440 was capable of utilizing ACC as its sole nitrogen source for growth on plates. Inoculation enhanced the depletion of available nitrogen, phosphorus, and potassium; increased bacterial diversity; improved the stability of the soil microbial community; and caused the mycelium of morels to grow earlier. These processes occurred along with a decline in the abundance of the Streptomyces genus. Furthermore, a positive correlation was identified between the abundance of P. putida and ACC deaminase activity in the soil. Overall, this study examined the role of Pseudomonas putida inoculation in modulating the soil microbial community and metabolic processes within casing soil during Morchella sextelata cultivation. The findings indicate that P. putida inoculation promotes Morchella growth through ACC decomposition and microbial restructuring, offering a potential strategy for mitigating ethylene-related suppression in continuous cropping systems. Full article

Infections caused by Staphylococcus aureus pose significant public health challenges, particularly due to antibiotic-resistant strains like MRSA. In this context, Streptomyces, a genus known for producing natural antibiotics, emerges as a promising source for novel therapeutic agents. In this study, a bibliometric analysis of the scientific literature (2015–2024) on Streptomyces as antibiotic biofactories against S. aureus was performed, aiming to identify publication trends, collaborative networks, and emerging research areas. Using the Web of Science database, searches were performed with descriptors (“Streptomyces” AND “Staphylococcus aureus”), including original articles and reviews in English. Data were analyzed with VOSviewer and Biblioshiny to visualize collaborative networks, keyword co-occurrences, and trends. A total of 755 articles from 3705 authors were analyzed, highlighting significant collaboration (98.7%). Publications showed marked growth, particularly in Microbiology (21.7%), Pharmacology and Pharmacy (16.8%), and Biotechnology and Applied Microbiology (16.1%). China and India led in publication volume, whereas the United States exhibited the highest citation impact. Key emerging research topics include biosynthesis and metabolic optimization, antimicrobial activity and bioprospecting, mechanisms of antibiotic action and bacterial resistance, and genomic analyses. Research on Streptomyces for antibiotic production against S. aureus demonstrates continuous expansion and global interest, emphasizing the importance of international collaboration and multidisciplinary approaches. Future studies should intensify exploration of biodiverse environments, genetic engineering applications, and combinatorial strategies to effectively address antimicrobial resistance. Full article

Microbial communities are known to colonize biocide-free (BFFs) and even biocide-containing façades (BCFs) under various environmental conditions, leading to loss of value of façades due to biologically caused aging and discoloration. The first objective of this study was to characterize the bacterial and fungal cultivation-based communities present on BCFs and BFFs after one year of outdoor exposure. The second objective was to assess their tolerance to biocide octylisothiazolinone (OIT), which was only present on the BCFs. Culture-based analysis revealed significant differences in bacterial community composition between the BFFs and BCFs. Fungal isolates also varied, with Penicillium predominantly found on the BCFs and Vishniacozyma and Memnoniella on the BFFs. MIC testing showed that the isolates from the BCFs exhibited slightly higher tolerance to OIT than those from the BFFs, although the differences were not statistically significant. Notably, several bacterial genera identified in both façade types—Clavibacter, Micrococcus, Nocardioides, Rhodococcus, and Streptomyces—as well as the fungal genus Penicillium, have previously been reported to degrade biocides. These findings demonstrate that both BF and BC façades support taxonomically diverse and resilient microbial communities within a relatively short exposure period. While minor shifts in biocide tolerance were observed, the lack of significant differences suggests that microbial adaptation to biocide-containing façades may be more complex and gradual, underscoring the need for time-resolved and functional studies to better understand microbial adaptation to biocide in façades. Full article

This study investigates the impact of post-volcanic gas emissions on soil microbial communities in the Băile Lăzărești region (Romania). Nineteen soil samples across a CO₂ gradient ranging from background levels to ≈46,221 ppm. Methane and hydrogen sulfide showed localized peaks (CH₄ up to 8271 ppm; H₂S up to ~10.12 ppm), with CH₄ contributing to outlier community patterns. eDNA metabarcoding identified 3064 OTUs, (2463 bacterial and 601 fungal). Bacteria were dominated by Proteobacteria, fungi by Ascomycota, with Thelebolales nearly ubiquitous. Alpha diversity (Chao1, Fisher) declined significantly in high-CO₂ soils (>3000 ppm), while intermediate concentrations (1000–3000 ppm) showed heterogeneous responses. Beta-diversity analyses (PCoA, clustering) revealed distinct grouping of high-CO₂ soils, with sample P16 (CH₄-rich) forming an outlier. A PCA including CO₂, CH₄, and H₂S confirmed CO₂ as the main driver of variance (>65%), with CH₄ accounting for local effects. At the genus level, Acidobacterium, Granulicella, Streptomyces, and Nocardia increased with CO₂, while Rhizobium and Pseudomonas declined. Fungal responses were mixed: Thelebolus and Cladosporium increased, whereas Mortierella and Cryptococcus decreased. Overall, elevated soil CO₂ reduced microbial richness and reorganized communities, while CH₄ shaped local niches. These findings provide key natural analog insights for assessing ecological risks of CO₂ leakage from geological storage. Full article

Mining novel Streptomyces species from extreme environments provides a valuable strategy for the discovery of new antibiotics. Here, we report a strain of Streptomyces sp. HMX87^T, which exhibits antimicrobial activity and was isolated from desert soil collected in the Tuha Basin, China. Molecular taxonomic analysis revealed that the 16S rRNA gene sequence of strain HMX87^T shares the highest similarity with those of Streptomyces bellus CGMCC 4.1376^T (98.5%) and Streptomyces coerulescens DSM 40146^T (98.43%). In phylogenetic trees, it formed a distinct branch. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain HMX87^T and the above two type strains were below the thresholds of 95% and 70%, respectively, confirming that strain HMX87^T represents a novel species within the genus Streptomyces, for which the name Streptomyces hamibioticus sp. nov. is proposed. Physiologically, the strain HMX87^T grew at temperatures ranging from 25 to 37 °C, tolerated pH values from 5 to 12, and survived in NaCl concentrations of 0% to 8% (w/v). Chemotaxonomic characterization indicated the presence of LL-diaminopimelic acid (LL-DAP) in the cell wall, ribose and galactose as whole-cell hydrolysate sugars, MK-9(H8) (66.3%) as the predominant menaquinone, and iso-C_16:0 (25.94%) and anteiso-C_15:0 (16.98%) as the major fatty acids characteristics that clearly distinguish it from its closest relatives. Whole-genome sequencing of strain HMX87^T revealed an abundance of genes associated with high-temperature tolerance, salt-alkali resistance, and antimicrobial activity. The genomic features and secondary metabolic potential reflect its adaptation to extreme environmental conditions, including high temperature, salinity, alkalinity, strong ultraviolet radiation, and oligotrophic nutrients. The strain HMX87^T has been deposited in the Czech Collection of Microorganisms (CCM 9454^T) and the Guangdong Microbial Culture Collection Center (GDMCC 4.391^T). The 16S rRNA gene and whole-genome sequences have been submitted to GenBank under accession numbers PQ182592 and PRJNA1206124, respectively. Full article

Antimicrobial resistance represents a critical global health challenge, intensifying the urgency of discovering novel antibiotics. Actinomycetota species, the most prolific source of clinical antibiotics, remain underexplored in unique ecosystems. In this study, we isolated 340 Actinomycetota strains from soils of the Brazilian semiarid Caatinga biome. Screening revealed that 122 isolates (35.9%) exhibited antimicrobial activity against clinically relevant pathogens (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans). Notably, 19 isolates showed activity against Mycobacterium tuberculosis H37Ra. MALDI-TOF MS analysis successfully provided genus-level identification for a subset of isolates, with approximately 32% assigned to the Streptomyces genus. However, the limited resolution of the database for the majority of the strains indicates high phylogenetic diversity and suggests the presence of potentially novel species. Metabolomic profiling via LC-MS/MS and GNPS molecular networking suggested the production of known antibiotics such as actinomycins, cyclomarins and anthracyclines and unveiled distinct molecular families putatively assigned to undescribed metabolites. Our work establishes the Caatinga biome as a valuable reservoir of bioactive Actinomycetota, encoding both known and potentially novel antimicrobial compounds. These results underscore the potential of underexplored and extreme environments in the quest to overcome antibiotic resistance. Full article

The purpose of this study was to investigate the taxonomic and phylogenomic placement of the proposed genus ‘Solwaraspora’ within the context of other marine genera using a dual-omics approach. Initially, we isolated bacteria from marine tunicates, squirts, and sponges, which were morphologically similar to an emerging genus (identified as ‘Micromonospora_E’ by the GTDB-tk2 database using whole genome sequence data) by colony shape, size, and clustering pattern, but only found five strains in our dataset belonging to this distinction. Due to the minimally explored nature of this genus, we sought to identify more bacterial strains with similar morphology to Micromonospora‘Micromonospora_E’ by whole genome sequencing (WGS). Within our collection, we noted 35 strains that met this criterion and extracted genomic information to perform WGS on these strains. With this information, we studied taxonomic and phylogenomic relationships among these organisms. Using the data gathered from WGS, we were able to identify an additional five strains labeled by the GTDB-tk2 database as Micromonospora‘Micromonospora_E’, as well as construct phylogenomic trees to examine the evolutionary relationships between these strains. ANI values were calculated between strains from our dataset and type strains of Micromonospora and Plantactinospora as well as against an outgroup Streptomyces strain. No type strains are available for ‘Solwaraspora’. Using MALDI-TOF MS, we positively identified ‘Solwaraspora’, which was supported by the phylogenomic tree showing Micromonospora’Micromonospora_E’ (‘Solwaraspora’) in a distinct clade from Plantactinospora and Micromonospora. Additionally, we discovered gene cluster families (GCFs) in alignment with genera, as well as a large representation of biosynthetic gene clusters (BGCs) coming from the ‘Solwaraspora’ strains. These findings suggest significant potential to discover novel chemistry from ‘Solwaraspora’, adding to the importance of investigating this new genus of bacteria. Full article

Bacterial natural ecological niches are characterized by variations in the availability of nutrients, resulting in a complex metabolism. Their impressive ability to adapt to changeable nutrient conditions is possible through the utilization of large amounts of substrates. Recent discoveries in bacterial metabolism have suggested the importance of polyamine metabolism in bacteria, particularly in those of the order Actinomycetales, in enabling them to survive in their natural habitats. This makes such enzymes promising targets to inhibit their growth. Since the polyamine metabolisms of soil bacteria of the genus Streptomyces and the human pathogenic Mycobacteria are surprisingly similar, target-based drug development in Streptomyces and Mycobacterium spp. is an alternative approach to the classical search for antibiotics. The recent development of drugs to treat epidemic diseases like tuberculosis (TB) has gained attention due to the occurrence of multidrug-resistant strains. In addition, drug repurposing plays a crucial role in the treatment of various complex diseases, such as malaria. With that notion, the treatment of TB could also benefit from this approach. For example, molecular chaperones, proteins that help other proteins to fold properly, are found in almost all living organisms, including the causative agents of TB. Therefore, targeting these molecules could help in the treatment of TB. We aim to summarize our knowledge of the nitrogen and carbon metabolism of the two closely related actinobacterial genera, Streptomyces and Mycobacterium, and of the identification of new potential drug targets. Full article

In recent years, there has been extensive documentation of pathogenic fungi infecting Morchella sextelata. However, investigations of microorganisms with antagonistic properties against these pathogens are limited. This study successfully isolated two isolates of the genus Streptomyces (F16 and F19) from the rhizosphere soil of M. sextelata fruiting bodies, both of which exhibit potent antagonistic activity against Pestalotiopsis trachicarpicola, the causative agent of M. sextelata wilt disease. Comprehensive characterization, including physiological–biochemical tests and 16S rDNA sequence analysis, led to the identification of these isolates as Streptomyces sp. F16 and Streptomyces sp. F19. Both isolates significantly inhibited P. trachicarpicola through multiple mechanisms. The volatile compounds produced by these isolates effectively suppressed the conidial germination of P. trachicarpicola in vitro. Furthermore, fermentation filtrates at various dilutions exhibited pronounced antifungal activity against conidial germination, with Streptomyces sp. F16 showing 66.93% inhibition at a 50× dilution and Streptomyces sp. F19 achieving 49.22% inhibition under identical conditions. Field experiments have demonstrated the practical applicability of these antagonists. The topical application of fermentation filtrates (diluted 50×) from both isolates significantly reduced the incidence and severity of disease in M. sextelata cultivation. Notably, the yield improvements were substantial: fields treated with Streptomyces sp. F16 produced 299.6 g/m², whereas those treated with Streptomyces sp. F19 yielded 277.65 g/m². These yields significantly surpassed those of both the untreated control group (231 g/m²) and the P. trachicarpicola-inoculated group (134.93 g/m²). These findings indicate that the two isolates not only effectively control P. trachicarpicola but also increase the yield of M. sextelata. Full article