Taxonomic Characterization, and Secondary Metabolite Analysis of Streptomyces triticiradicis sp. nov.: A Novel Actinomycete with Antifungal Activity

Streptomyces adonidis sp. nov., a novel actinomycete strain with antifungal activity isolated from the root of Adonis amurensis Regel

A novel endophytic actinomycete with antagonistic activity against Fusarium moniliforme, designated strain NEAU-BLH26T, was isolated from the root of Adonis amurensis Regel collected at the horticultural experiment station of Northeast Agricultural University, Heilongjiang Province, northeast China. Strain NEAU-BLH26T exhibited morphological and chemotaxonomic features of the genus Streptomyces. The diamino acid present in its cell wall was identified as LL-diaminopimelic acid, while galactose detected in whole-cell hydrolysates. The menaquinones were identified as MK-9(H6), MK-9(H8), and MK-9(H4). The phospholipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified aminolipids. The major fatty acids were determined to be iso-C16:0 and C16:0. The DNA G + C content, based on the genome sequence, was 70.5 mol%. Phylogenetic analyses of 16S rRNA gene and whole genome sequences analyses indicated that strain NEAU-BLH26T was most closely related to Streptomyces geranii A301T, with a 16S rRNA gene sequence similarity of 98.69%. However, the average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values confirmed that strain NEAU-BLH26T represents a distinct species. This conclusion was further supported by phenotypic and chemotaxonomic differences between strain NEAU-BLH26T and its closest relative. Additionally, the secondary metabolite biosynthetic gene clusters in strain NEAU-BLH26T were predicted and analyzed. Based on phenotypic, chemotaxonomic and genotypic evidence, strain NEAU-BLH26T is proposed as a novel species of the genus Streptomyces, for which the name Streptomyces adonidis sp. nov. is suggested. The type strain is NEAU-BLH26T (= JCM 36414T = MCCC 1K08678T).

Evaluation of Streptomyces sporoverrucosus B-1662 for biological control of red pepper anthracnose and apple bitter rot diseases in Korea

Fungi are the prominent phytopathogens that have significant impact on the productivity of agriculture worldwide. Streptomyces species have been extensively studied for the production of various bioactive metabolites. These metabolites have been used as biocontrol agents for the management of diseases caused by phytopathogenic fungi. The purpose of this investigation is to assess the efficacy of Streptomyces sporoverrucosus B-1662, an antagonistic agent in the control of red pepper anthracnose caused by Colletotrichum acutatum KACC 42403 and apple anthracnose caused by Colletotrichum siamense CGCP6 (GYUN-10348). On the basis of the morphological, and molecular characterization using 16S rRNA, the strain B-1662 was determined to be S. sporoverrucosus. The strain B-1662 exhibited antagonistic activity against seven fungal phytopathogens, including C. acutatum KACC 42403 and C. siamense CGCP6. The culture filtrates (CF) from B-1662 showed antifungal activity against all seven fungal pathogens with greater inhibition rate (%) in comparison with a control. The bacterial suspensions of B-1662 showed an excellent biological control effect on the red pepper anthracnose and apple bitter rot using an in planta assay. The anthracnose disease rate (%) was controlled by over 90% with B-1662 cell suspensions at 105 to 107 CFU/mL. Compared to a control, the strain B-1662 played a more effective role in controlling the anthracnose disease in field conditions in both years 2022 and 2023. From the effective solvent fractions, the effect compound (dibutoxybutane) has been isolated exhibiting with antifungal effect. The genetic base underlying the biocontrol traits of B-1662 was characterized using the whole-genome sequence of B-1662, which was compared with closely related strains. Consequently, these results collectively suggest that S. sporoverrucosus B-1662 can aid in the management of red-pepper anthracnose.

Metabonomic analysis to identify exometabolome changes underlying antifungal and growth promotion mechanisms of endophytic Actinobacterium Streptomyces albidoflavus for sustainable agriculture practice

In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties. The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture.

Identification of bioactive compounds of Bacillus velezensis HNA3 that contribute to its dual effects as plant growth promoter and biocontrol against post-harvested fungi

IMPORTANCE

The current study is an extension to our previous work on the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis HNA3 strain, which comes to confirm and reveals the huge stock of active secondary metabolites produced by HNA3. HNA3-emitted volatile organic compounds (VOCs) have demonstrated the capacity to impede the growth of phytopathogens affecting some fruits and vegetables, even in the absence of direct contact. Additionally, these volatiles enhanced soybean seed germination by breaking seed dormancy and inducing root system development. Furthermore, they promoted seedling growth, giving it prominence in soybean cultivation. The relevance of active volatiles derives from the fact that they can be developed as natural-safe biocontrol agents and plant promoters. This research validates the remarkable bioactivities exhibited by the Bacillus velezensis HNA3 and their potential applications in agriculture as an inoculant, encompassing biocontrol, plant growth promotion, and seed germination activities, thereby offering a safer alternative to hazardous chemicals.

Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor

BACKGROUND

Oviedomycin is one among several polyketides known for their potential as anticancer agents. The biosynthetic gene cluster (BGC) for oviedomycin is primarily found in Streptomyces antibioticus. However, because this BGC is usually inactive under normal laboratory conditions, it is necessary to employ systematic metabolic engineering methods, such as heterologous expression, refactoring of BGCs, and optimization of precursor biosynthesis, to allow efficient production of these compounds.

RESULTS

Oviedomycin BGC was captured from the genome of Streptomyces antibioticus by a newly constructed plasmid, pCBA, and conjugated into the heterologous strain, S. coelicolor M1152. To increase the production of oviedomycin, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system was utilized in an in vitro setting to refactor the native promoters within the ovm BGC. The target promoters of refactoring were selected based on examination of factors such as transcription levels and metabolite profiling. Furthermore, genome-scale metabolic simulation was applied to find overexpression targets that could enhance the biosynthesis of precursors or cofactors related to oviedomycin production. The combined approach led to a significant increase in oviedomycin production, reaching up to 670 mg/L, which is the highest titer reported to date. This demonstrates the potential of the approach undertaken in this study.

CONCLUSIONS

The metabolic engineering approach used in this study led to the successful production of a valuable polyketide, oviedomycin, via BGC cloning, promoter refactoring, and gene manipulation of host metabolism aided by genome-scale metabolic simulation. This approach can be also useful for the efficient production of other secondary molecules encoded by 'silent' BGCs.

A Rhizobacterium, Streptomyces albulus Z1-04-02, Displays Antifungal Activity against Sclerotium Rot in Mungbean

Sclerotium rot causes damping-off and stem rot in seedlings and mature mungbeans, which negatively impacts cultivation. The use of a rhizobacterium to control soil-borne diseases is an alternative method to the excess use of synthetic fungicides; therefore, this study aims to screen rhizosphere actinobacteria with fungicidal activities against Sclerotium rolfsii, the pathogen that causes sclerotium rot in mungbeans. Primary screening showed that the Streptomyces sp. isolate Z1-04-02 displayed the highest effectiveness against S. rolfsii in dual culture plates, with a percentage inhibition of 74.28%. An assay containing enzymes that degrade cell walls, of the cell-free culture filtrate (CF) of Z1-04-02, showed that the activities of chitinase and β-1,3-glucanase were 0.0209 and 1.0210 U/mL, respectively, which was significantly higher than that of the control (media alone). The cell-free CF of Z1-04-02, incubated at 37 °C and 100 °C, using agar well diffusion, effectively inhibited the growth of S. rolfsii with inhibition percentages of 37.78% and 27.78%, respectively. Solid-phase microextraction (SPME) was applied to trap volatiles released from Z1-04-02 and gas chromatography-mass spectrometry (GC/MS); volatile antifungal compounds were tentatively identified as bicyclic monoterpene (1R)-(-)-myrtenal. The application of the cell-free CF, and the spore suspension of Z1-04-02, showed disease severity indexes (DSIs) of 12.5% and 8.25%, respectively, which were significantly lower than those showing inoculation by S. rolfsii alone. The identification of this strain by morphology, biochemistry tests, and 16s rDNA sequences revealed that Z1-04-02 was Streptomyces albulus. This finding revealed that S. albulus Z1-04-02 displayed diverse fungicidal activities against S. rolfsii, and it has the potential to act as a biological control agent in terms of inhibiting sclerotium rot in mungbeans.

Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function

Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin

Streptomyces rapamycinicus NRRL 5491 is a well-known producer of rapamycin, a secondary metabolite with useful bioactivities, including antifungal, antitumor, and immunosuppressive functions. For the enhanced rapamycin production, a rapamycin-overproducing strain SRMK07 was previously obtained as a result of random mutagenesis. To identify genomic changes that allowed the SRMK07 strain’s enhanced rapamycin production, genomes of the NRRL 5491 and SRMK07 strains were newly sequenced in this study. The resulting genome sequences of the wild-type and SRMK07 strains showed the size of 12.47 Mbp and 9.56 Mbp, respectively. Large deletions were observed at both end regions of the SRMK07 strain’s genome, which cover 17 biosynthetic gene clusters (BGCs) encoding secondary metabolites. Also, genes in a genomic region containing the rapamycin BGC were shown to be duplicated. Finally, comparative metabolic network analysis using these two strains’ genome-scale metabolic models revealed biochemical reactions with different metabolic fluxes, which were all associated with NADPH generation. Taken together, the genomic and computational approaches undertaken in this study suggest biological clues for the enhanced rapamycin production of the SRMK07 strain. These clues can also serve as a basis for systematic engineering of a production host for further enhanced rapamycin production.

Recently Discovered Secondary Metabolites from Streptomyces Species

The Streptomyces genus has been a rich source of bioactive natural products, medicinal chemicals, and novel drug leads for three-quarters of a century. Yet studies suggest that the genus is capable of making some 150,000 more bioactive compounds than all Streptomyces secondary metabolites reported to date. Researchers around the world continue to explore this enormous potential using a range of strategies including modification of culture conditions, bioinformatics and genome mining, heterologous expression, and other approaches to cryptic biosynthetic gene cluster activation. Our survey of the recent literature, with a particular focus on the year 2020, brings together more than 70 novel secondary metabolites from Streptomyces species, which are discussed in this review. This diverse array includes cyclic and linear peptides, peptide derivatives, polyketides, terpenoids, polyaromatics, macrocycles, and furans, the isolation, chemical structures, and bioactivity of which are appraised. The discovery of these many different compounds demonstrates the continued potential of Streptomyces as a source of new and interesting natural products and contributes further important pieces to the mostly unfinished puzzle of Earth’s myriad microbes and their multifaceted chemical output.

Streptomyces typhae sp. nov., a novel endophytic actinomycete with antifungal activity isolated the root of cattail (Typha angustifolia L.)

A novel endophytic actinomycete with antagonistic activity against various phytopathogenic fungi, designated strain p1417^T, was isolated from the root of cattail (Typha angustifolia L.) collected from Yunnan Province, Southwest China. A polyphasic taxonomic study was carried out to establish the taxonomic status of this strain. Strain p1417^T was found to have morphological and chemotaxonomic characteristics typical of the genus Streptomyces. The diamino acid present in the cell wall was LL-diaminopimelic acid. Xylose and arabinose occurred in whole cell hydrolysates. The menaquinones were identified as MK-9(H₈), MK-9(H₆) and MK-9(H₄). The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were found to be iso-C_16:0, anteiso-C_15:0, iso-C_15:0 and C_16:0. The genomic DNA G + C content of strain p1417^T based on the genome sequence was 72.0 mol%. Based on 16 S rRNA gene, five housekeeping genes and whole genome sequences analysis, strain p1417^T was most closely related to Streptomyces flavofungini JCM 4753^T (99.4% 16 S rRNA gene sequence similarity), Streptomyces alboflavus JCM 4615^T (98.8%) and Streptomyces aureoverticillatus JCM 4347^T (98.2%). However, the average nucleotide identity values, the digital DNA-DNA hybridization values and the multilocus sequence analysis evolutionary distances between this strain and its closely related strains showed that it belonged to one distinct species. In addition, these results were also supported by differences in the phenotypic and chemotaxonomic characteristics between strain p1417^T and three closely related type strains. Therefore, it is concluded that strain p1417^T represents a novel species of the genus of Streptomyces, for which the name Streptomyces typhae sp. nov. is proposed. The type strain is p1417^T (= CCTCC AA 2019091^T = DSM 110636^T).

Discovery of Frenolicin B as Potential Agrochemical Fungicide for Controlling Fusarium Head Blight on Wheat

In this study, the supernatant extract from fermentation broth of Streptomyces sp. NEAU-H3 showed strong antifungal activity against Fusarium graminearum strain PH-1 in vitro and in vivo. Three known pyranonaphthoquinones were isolated by means of an activity-guided method, and frenolicin B was characterized as the main active ingredient. Frenolicin B displayed strong antifungal activity against F. graminearum strain PH-1 with an EC₅₀ value of 0.51 mg/L, which is lower than that of carbendazim (0.78 mg/L) but higher than that of phenamacril (0.18 mg/L). Frenolicin B could also strongly inhibit the mycelial growth of Fusarium species, including F. graminearum and F. asiaticum, as well as carbendazim-resistant Fusarium strains isolated from field, with EC₅₀ values of 0.25-0.92 mg/L. Results from field experiments showed that the efficacy of frenolicin B in controlling Fusarium head blight at a treatment concentration of 75 g ai/ha was better than those of phenamacril (375 g ai/ha) and carbendazim (600 g ai/ha) or had no significant difference with that of phenamacril (375 g ai/ha) in 2 years. Scanning electron microscope and transmission electron microscope observations revealed that after treating F. graminearum mycelia with frenolicin B, the mycelia appeared aberrant and had an uneven thickness and swelling, the cytoplasm had disintegrated, and some cell contents were lost. Transcriptome analysis suggests that frenolicin B might inhibit the metabolism of nucleotides and energy by affecting genes involved in phosphorus utilization but did not affect the expression of myosin 5, which is the specific target of phenamacril. These findings indicate that frenolicin B may be a potential agrochemical fungicide for controlling Fusarium head blight.

Recent Advances in the Chemistry of Bioactive Compounds from Plants and Soil Microbes: a Review

Bioactive compounds derived from plants and microbial sources are required for the survival of the human race and groundbreaking research must continue in this line. Plants and microbes are the major sources of naturally occurring bioactive compounds for numerous biotechnological applications. Recent progress in the fields of bioactive compounds and soil chemistry in agriculture has since given man a lead to the discovery of potent drugs that combat both human and plant diseases. The soil provides the medium for the growth of medicinal plants, but its contamination greatly affects the quality of drugs, food crops, and other essential elements present in the plants which give strength to the body. This area has attracted the attention of scientists and the drug industry toward developing more potent drugs from medicinal plants grown in different soil. The studies of the effect of various parameters and the properties of soil such as; effect of heavy metals, pH, soil organic matter, and phytoremediation process have given a measure of some quality dependence of the soil producing secondary metabolites and soil containing microbes. The information provided will be useful in determine the action of microbes and their interaction with the soil and all true plants producing drugs. Some active compounds in plants and microbes, their properties, and applications have been described in this review. The soil microbes, activities and their interactions, effects of soil particle size, dispersibility and stability of microbes in the soil, and the future outlook for the development of novel active compounds have been reported.

Characterization of a Novel Endophytic Actinomycete, Streptomyces physcomitrii sp. nov., and Its Biocontrol Potential Against Ralstonia solanacearum on Tomato

Bacterial wilt of tomato is a destructive disease caused by Ralstonia solanacearum throughout the world. An endophytic actinomycete with antagonistic activity, designated strain LD120^T, was isolated from moss (Physcomitrium sphaericum (Ludw) Fuernr). The biocontrol test demonstrated that co-inoculation by the isolate and the pathogen gave the greatest biocontrol efficiency of 63.6%. Strain LD120^T had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces. The diamino acid present in the cell wall was LL-diaminopimelic acid. Arabinose, glucose, rhamnose, and ribose occured in whole cell hydrolysates. The menaquinones detected were MK-9(H₄), MK-9(H₆), MK-9(H₈), and MK-9(H₂). The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylinositol. The major cellular fatty acids were found to be iso-C_16:0, iso-C_17:0, anteiso-C_15:0, and C_16:1 ω7c. The DNA G+C content of the draft genome sequence, consisting of 7.6 Mbp, was 73.1%. Analysis of the 16S rRNA gene sequence showed that strain LD120^T belongs to the genus Streptomyces, with the highest sequence similarity to Streptomyces azureus NRRL B-2655^T (98.97%), but phylogenetically clustered with Streptomyces anandii NRRL B-3590^T (98.62%). Multilocus sequence analysis based on five other house-keeping genes (atpD, gyrB, rpoB, recA, and trpB) and the low level of DNA–DNA relatedness, as well as phenotypic differences, allowed strain LD120^T to be differentiated from its closely related strains. Therefore, the strain was concluded to represent a novel species of the genus Streptomyces, for which the name Streptomycesphyscomitrii sp. nov. was proposed. The type strain was LD120^T (=CCTCC AA 2018049^T = DSM 110638^T).

Characterization of Streptomyces piniterrae sp. nov. and Identification of the Putative Gene Cluster Encoding the Biosynthesis of Heliquinomycins

A novel actinomycete producing heliquinomycin and 9’-methoxy-heliquinomycin, designated strain jys28^T, was isolated from rhizosphere soil of Pinus yunnanensis and characterized using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces. It formed spiral chains of spores with spiny surfaces. The menaquinones detected were MK-9(H₆), MK-9(H₈) and MK-9(H₄). The major fatty acids were iso-C_16:0, C_15:0, C_16:1ω7с and anteiso-C_15:0. The phospholipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylinositol mannoside. The DNA G + C content of the draft genome sequence, consisting of 8.5 Mbp, was 70.6%. Analysis of the 16S rRNA gene sequence showed that strain jys28^T belongs to the genus Streptomyces with the highest sequence similarities to Streptomyces chattanoogensis NBRC 13058^T (99.2%) and Streptomyces lydicus DSM 40002^T (99.2%) and phylogenetically clustered with them. Multilocus sequence analysis based on five other house-keeping genes (atpD, gyrB, rpoB, recA and trpB) and the low level of DNA–DNA relatedness and phenotypic differences allowed the novel isolate to be differentiated from its most closely related strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomycespiniterrae sp. nov. is proposed. Furthermore, the putative biosynthetic gene cluster of heliquinomycins was identified and the biosynthetic pathway was discussed. The type strain is jys28^T (=CCTCC AA 2018051^T =DSM 109823^T).