Search Results (15)

Actinomycetes are among the richest sources of bioactive secondary metabolites in biotechnology, owing to their remarkable metabolic diversity. Although the genus Streptomyces has been extensively explored and has yielded many clinically important antibiotics, rare actinomycetes remain comparatively underinvestigated. In this study, Kitasatospora sp. SeTe27, isolated from uncontaminated soil in Sicily (Italy), was investigated for its antibacterial activity and fermentation-driven enhancement of secondary metabolite production. The strain inhibited Staphylococcus aureus ATCC 25923, prompting physiological and genomic analyses. Spore conditioning was evaluated in four media (R5A, GYM, TSB, and YEME) to enhance antibiotic production. Conditioned cultures exhibited markedly increased antibacterial activity in TSB and YEME, moderate production in R5A, and no detectable activity in GYM. Whole-genome sequencing revealed an 8.5 Mb genome (73.5% GC) containing 48 biosynthetic gene clusters (BGCs), including NRPS, PKS, terpene, and hybrid pathways. Several clusters showed high similarity to known antibiotic-associated BGCs, such as clifednamide- and phenazine-related pathways, while numerous orphan clusters indicated significant unexplored biosynthetic potential. These findings identify Kitasatospora sp. SeTe27 as a promising antimicrobial producer and demonstrate that spore conditioning in complex media is an effective strategy to enhance antibiotic production in rare actinomycetes. Full article

The actinobacterial strain Kitasatospora griseola JNUCC 62 was isolated from volcanic wetland soil at Mulyeongari Oreum, Jeju Island, and taxonomically identified through 16S rRNA gene and whole-genome analyses. The complete genome, assembled from PacBio Sequel I reads, spans 8.31 Mb with a GC content of 72.8% and contains 7265 coding sequences. Comparative genomic indices (Average nucleotide identity, ANI 97.46%; digital DNA–DNA hybridization, dDDH 84.4%) confirmed its conspecific relationship with K. griseola JCM 3339^T. Genome mining using antiSMASH 8.0 revealed 30 biosynthetic gene clusters (BGCs), including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), ribosomally synthesized and post-translationally modified peptide (RiPP), lanthipeptide, and terpene types, accounting for 18.6% of the genome. Several BGCs displayed homology to known formicamycin-, lankacidin-, and lanthipeptide-type clusters, while others were novel or cryptic, reflecting adaptation to the nutrient-poor volcanic environment. Ethyl acetate extraction of the culture broth, especially under tryptophan-supplemented conditions, yielded four metabolites—1-acetyl-β-carboline, perlolyrine, tryptopol, and 1H-pyrrole-2-carboxylic acid—identified by UV and NMR spectroscopy. These compounds correspond to NRPS–PKS hybrid and arylpolyene-type gene clusters predicted in the genome, suggesting precursor-directed biosynthesis of indole and pyrrole alkaloids. The ethyl acetate extract (JNUCC62 EA) exhibited strong antioxidant capacity in the ABTS assay, anti-inflammatory activity via inhibition of nitric oxide (31.09 ± 3.69% of control) and cytokines (IL-6, IL-1β, TNF-α) in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, and anti-melanogenic effects in α-melanocyte-stimulating hormone (MSH)-stimulated B16F10 melanoma cells, where melanin content and tyrosinase activity decreased to 61.49 ± 1.24% and 24.32 ± 0.31% of the control, respectively, without cytotoxicity. A human primary skin irritation test confirmed no irritation up to 50 µg/mL, establishing excellent dermal safety. Collectively, these findings highlight K. griseola JNUCC 62 from Mulyeongari Oreum as a volcanic wetland-derived actinomycete harboring rich biosynthetic potential for novel indole alkaloids with antioxidant, anti-inflammatory, and whitening properties, supporting its development as a safe and multifunctional cosmeceutical ingredient. Full article

Plant growth-promoting bacteria (PGPB) associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner offer a viable strategy to reduce synthetic inputs and enhance resilience in coffee agroecosystems. This review synthesizes evidence from the past decade on rhizosphere-associated and endophytic taxa, their plant growth-promotion and biocontrol mechanisms and the resulting agronomic outcomes. A compartment-specific core microbiome is reported, in the rhizosphere of both hosts, in which Bacillus and Pseudomonas consistently dominate. Within endophytic communities, Bacillus predominates across tissues (roots, leaves and seeds), whereas accompanying genera are host- and tissue-specific. In C. arabica, endophytes frequently include Pseudomonas in roots and leaves. In C. canephora, root endophytes recurrently include Burkholderia, Kitasatospora and Rahnella, while seed endophytes are enriched for Curtobacterium. Functionally, coffee-associated PGPB solubilize phosphate; fix atmospheric nitrogen via biological nitrogen fixation; produce auxins; synthesize siderophores; and express 1-aminocyclopropane-1-carboxylate deaminase. Indirect benefits include the production of antifungal and nematicidal metabolites, secretion of hydrolytic enzymes and elicitation of induced systemic resistance. Under greenhouse conditions, inoculation with PGPB commonly improves germination, shoot and root biomass, nutrient uptake and tolerance to drought or nutrient limitation. Notable biocontrol activity against fungal phytopathogens and plant-parasitic nematodes has also been documented. Key priorities for translation to practice should include (i) multi-site, multi-season field trials to quantify performance, persistence and economic returns; (ii) strain-resolved omics to link taxa to functions expressed within the plant host; (iii) improved bioformulations compatible with farm management and (iv) rationally designed consortia aligned with production goals and biosafety frameworks. Full article

Biological control is considered one of the most important methods for preventing and controlling the worldwide fungal disease gray mold, caused by Botrytis cinerea. Among the various agents used in biological control, actinomycetes represent a significant group of microorganisms that offer valuable resources for biocontrol strategies. In this study, a total of 132 actinomycetes, belonging to four genera (Streptomyces, Kitasatospora, Amycolatopsis, and Nocardia), were isolated from soil. Among the five media tested, ISP-2 and GS NO.1 media were found to be highly suitable for isolating actinomycetes. It is worth mentioning that the strain TCS21-117 displayed significant inhibitory effects against Botrytis cinerea and nine other pathogenic fungi. The strain TCS21-117 was identified as Streptomyces roietensis by its morphological characteristics and phylogenetic analysis of the 16S rRNA gene. The optimum culture conditions for the strain TCS21-117 were a potato dextrose broth medium at an initial pH of 8.0, a liquid volume of 125 mL in a 250 mL flask, 180 r·min⁻¹ at 28 °C, and an inoculum size of 1% for 7 days. Under these conditions, the inhibition rate against Botrytis cinerea was 93.31%, a significant increase (31.98%) as compared to the control. Notably, the antifungal compounds produced by the strain TCS21-117 exhibited strong stability across a range of temperatures, pH levels, and durations of storage and UV irradiation. This study showed that the Streptomyces roietensis strain TCS21-117 had strong inhibitory activity against Botrytis cinerea under optimized fermentation conditions, enriching the microbial resources for gray mold control. Full article

Bacterial wilt, caused by Ralstonia solanacearum, is one of the main challenges for sustainable tomato production in the Amazon region. This study evaluated the potential of bacteria isolated from sediments of the Solimões and Negro rivers for the biocontrol of this disease. From 36 bacteria selected through in vitro antibiosis, three promising isolates were identified: Priestia aryabhattai RN 11, Streptomyces sp. RN 24, and Kitasatospora sp. SOL 195, which inhibited the growth of the phytopathogen by 100%, 87.62%, and 100%, respectively. These isolates also demonstrated the ability to produce extracellular enzymes and plant growth-promoting compounds, such as indole-3-acetic acid (IAA), siderophore, and ammonia. In plant assays, during both dry and rainy seasons, P. aryabhattai RN 11 reduced disease incidence by 40% and 90%, respectively, while promoting the growth of infected plants. Streptomyces sp. RN 24 and Kitasatospora sp. SOL 195 exhibited high survival rates (85–90%) and pathogen suppression in the soil (>90%), demonstrating their potential as biocontrol agents. This study highlights the potential of Amazonian bacteria as biocontrol agents against bacterial wilt, contributing to the development of sustainable management strategies for this important disease. Full article

Actinomycetes have long been recognized as important sources of clinical antibiotics. However, the exploration of rare actinomycetes, despite their potential for producing bioactive molecules, has remained relatively limited compared to the extensively studied Streptomyces genus. The extensive investigation of Streptomyces species and their natural products has led to a diminished probability of discovering novel bioactive compounds from this group. Consequently, our research focus has shifted towards less explored actinomycetes, beyond Streptomyces, with particular emphasis on Kitasatospora setae (K. setae). The genome of K. setae was annotated and analyzed through whole-genome sequencing using multiple bio-informatics tools, revealing an 8.6 Mbp genome with a 74.42% G + C content. AntiSMASH analysis identified 40 putative biosynthetic gene clusters (BGCs), approximately half of which were recessive and unknown. Additionally, metabolomic mining utilizing mass spectrometry demonstrated the potential for this rare actinomycete to generate numerous bioactive compounds such as glycosides and macrolides, with bafilomycin being the major compound produced. Collectively, genomics- and metabolomics-based techniques confirmed K. setae’s potential as a bioactive secondary metabolite producer that is worthy of further exploration. Full article

The genus Streptomyces is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified according to recent molecular-based taxonomies. Recent developments of molecular-based analysis methods and availability of whole genome sequences of type strains enables researchers to reclassify these phylogenetically complex members on a large scale. This review introduces reclassifications of the genus Streptomyces reported in the past decade. Appropriately 34 Streptomyces species were transferred to the other genera, such as Kitasatospora, Streptacidiphilus, Actinoalloteichus and recently proposed new genera. As a result of reclassifications of 14 subspecies, the genus Streptomyces includes only four subspecies at present in practice. A total of 63 species were reclassified as later heterotypic synonyms of previously recognized species in 24 published reports. As strong relationships between species and the secondary metabolite-biosynthetic gene clusters become clarified, appropriate classifications of this genus will not only contribute to systematics, but also provide significant information when searching for useful bioactive substances. Full article

Lignin degradation in fungal systems is well characterized. Recently, a potential for lignin depolymerization and modification employing similar enzymatic activities by bacteria is increasingly recognized. The presence of genes annotated as peroxidases in Actinobacteria genomes suggests that these bacteria should contain auxiliary enzymes such as flavin-dependent carbohydrate oxidoreductases. The only auxiliary activity subfamily with significantly similar representatives in bacteria is pyranose oxidase (POx). A biological role of providing H₂O₂ for peroxidase activation and reduction of radical degradation products suggests an extracellular localization, which has not been established. Analysis of the genomic locus of POX from Kitasatospora aureofaciens (KaPOx), which is similar to fungal POx, revealed a start codon upstream of the originally annotated one, and the additional sequence was considered a putative Tat-signal peptide by computational analysis. We expressed KaPOx including this additional upstream sequence as well as fusion constructs consisting of the additional sequence, the KaPOx mature domain and the fluorescent protein mRFP1 in Streptomyces lividans. The putative signal peptide facilitated secretion of KaPOx and the fusion protein, suggesting a natural extracellular localization and supporting a potential role in providing H₂O₂ and reducing radical compounds derived from lignin degradation. Full article

The purpose of this study was to investigate the effects of chemically protected sodium butyrate (CSB) on growth performance and the early development and function of small intestine in broilers as one potential substitute for antibiotics. A total of 192 one-day-old Arbor Acres male broilers were randomly assigned into three dietary treatment groups (eight replicates per treatment): the control (CON) diet; ANT diet, CON diet supplemented with the antibiotics (enramycin, 8 mg/kg and aureomycin, 100 mg/kg); CSB diet, CON diet supplemented with 1000 mg/kg CSB, respectively. The results showed that dietary CSB and antibiotics addition significantly improved the growth performance of broilers by increasing the body weight gain (BWG) and feed conversion ratio (FCR) during different stages (p < 0.05). On day 21, the supplement of CSB in diet improved the structure of small intestine (duodenum, jejunum, and ileum) in broilers by increasing the ratio of villus height to crypt depth (VH/CD) (p < 0.05) and enhanced the butyric acid (BA) (p < 0.05) and total short chain fatty acids (SCFA) concentrations of small intestine (jejunum and ileum) compared with the CON and ANT diets. Besides that, the superoxide dismutase (SOD), total antioxidant capacity (TAC) and TAC to malondialdehyde (TAC/MDA) ratio of the ileal and jejunal mucosa were significantly higher (p < 0.05) in the CSB and ANT than in the CON. In addition, the supplement of CSB in diet markedly significantly enhanced α-amylase, lipase, and trypsin activities of the ileum (p < 0.05) as compared to the ANT diet. 16S rRNA gene sequencing indicated that CSB markedly increased the microbiota diversity of ileum in broilers at 21 days of age as compared to CON and ANT (p < 0.05). Furthermore, we found that Firmicutes was the predominant phyla and Lactobacillus was the major genus in the ileum of broilers. Compared with the ANT diet, the supplement of CSB in diet increased the relative abundance of some genera microbiota (e.g., Candidatus_Arthromitus, Romboutsia) by decreasing the relative abundance of Lactobacillus. Moreover, Akkermansia in the CSB was the highest in comparison to that in the CON and ANT. In addition, Kitasatospora that belongs to the phylum Actinobacteriota was only found in ileum of broilers fed the ANT diet. In summary, the supplement of 1000 mg/kg CSB in the diet improved the growth performance by promoting early development and function of the small intestine, which is associated with the regulation of intestinal flora and reestablishment of micro-ecological balance in broilers. Thus, CSB has great potential value as one of effective substitutes for in-feed antibiotics in the broiler industry. Full article

Naringenin and its glycosylated derivative naringin are flavonoids that are synthesized by the phenylpropanoid pathway in plants. We found that naringenin is also formed by the actinobacterium Streptomyces clavuligerus, a well-known microorganism used to industrially produce clavulanic acid. The production of naringenin in S. clavuligerus involves a chalcone synthase that uses p-coumaric as a starter unit and a P₄₅₀ monoxygenase, encoded by two adjacent genes (ncs-ncyP). The p-coumaric acid starter unit is formed by a tyrosine ammonia lyase encoded by an unlinked, tal, gene. Deletion and complementation studies demonstrate that these three genes are required for biosynthesis of naringenin in S. clavuligerus. Other actinobacteria chalcone synthases use caffeic acid, ferulic acid, sinapic acid or benzoic acid as starter units in the formation of different antibiotics and antitumor agents. The biosynthesis of naringenin is restricted to a few Streptomycess species and the encoding gene cluster is present also in some Saccharotrix and Kitasatospora species. Phylogenetic comparison of S. clavuligerus naringenin chalcone synthase with homologous proteins of other actinobacteria reveal that this protein is closely related to chalcone synthases that use malonyl-CoA as a starter unit for the formation of red-brown pigment. The function of the core enzymes in the pathway, such as the chalcone synthase and the tyrosine ammonia lyase, is conserved in plants and actinobacteria. However, S. clavuligerus use a P₄₅₀ monooxygenase proposed to complete the cyclization step of the naringenin chalcone, whereas this reaction in plants is performed by a chalcone isomerase. Comparison of the plant and S. clavuligerus chalcone synthases indicates that they have not been transmitted between these organisms by a recent horizontal gene transfer phenomenon. We provide a comprehensive view of the molecular genetics and biochemistry of chalcone synthases and their impact on the development of antibacterial and antitumor compounds. These advances allow new bioactive compounds to be obtained using combinatorial strategies. In addition, processes of heterologous expression and bioconversion for the production of naringenin and naringenin-derived compounds in yeasts are described. Full article

Experiments were carried out in soil microcosms with the treatment of pesticide formulations—imidacloprid, benomyl, and metribuzin in single and tenfold application rates. For additional stimulation of microorganisms, a starch–mineral mixture was added to some variants. For all samples, high-throughput sequencing on the Illumina MiSeq platform of the V4 (16S rRNA) and ITS1 (18S rRNA) fragments was carried out. As a result, it was possible to establish the characteristic changes in the structure of the soil fungal and bacterial communities under pesticides application. The application of pesticides was accompanied by dramatic shifts in alfa-diversity of the fungal community. The phylum Basidiomycota was likely to be involved in the degradation of pesticides. The changes in the relative abundance of the genera Terrabacter, Kitasatospora, Streptomyces, Sphingomonas, Apiotrichum, Solicoccozyma, Gamsia, and Humicola can be proposed as an indicator of pesticide contamination. It is suggested to use these markers for large-scale assessment of the effect of pesticides on soil microbial communities instead of classical integral methods, including within the framework of state registration of pesticides. It is also recommended to research the effect of pesticides on the soil microbiome during artificially initiated successions using the additional source of carbon. Full article

With its premium wood quality and resistance to pests, teak is a valuable tree species remarkably required for timber trading and agroforestry. The nursery stage of teak plantation needs critical care to warrant its long-term productivity. This study aimed to search for beneficial teak rhizosphere microbes and assess their teak-growth-promoting potentials during nursery stock preparation. Three teak rhizosphere/root-associated microbes, including two teak rhizobacteria (a nitrogen-fixing teak root endophyte-Agrobacterium sp. CGC-5 and a teak rhizosphere actinobacterium-Kitasatospora sp. TCM1-050) and an arbuscular mycorrhizal fungus (Claroideoglomus sp. PBT03), were isolated and used in this study. Both teak rhizobacteria could produce in vitro phytohormones (auxins) and catalase. With the pot-scale assessments, applying these rhizosphere microbes in the form of consortia offered better teak-growth-promoting activities than the individual applications, supported by significantly increased teak seedling biomass. Moreover, teak-growth-promoting roles of the arbuscular mycorrhizal fungus were highly dependent upon the support by other teak rhizobacteria. Based on our findings, establishing the synergistic interactions between beneficial rhizosphere microbes and teak roots was a promising sustainable strategy to enhance teak growth and development at the nursery stage and reduce chemical inputs in agroforestry. Full article

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

Previous studies have revealed that biochar could induce the disturbance of a microbial community above the family level. So far, very little is known about how individual bacteria are affected by biochar at genus or species levels. In this study, effects of biochar and its water-soluble compounds on the growth of individual soil bacteria were examined. Biochar derived from different feedstock showed disproportionate impacts on bacterial growth. Corncob biochar could significantly stimulate the growth of most tested strains, whereas the growth of four strains, including Bacillus pumilus ACCC04306 (Agricultural Culture Collection of China, ACCC), B. licheniformis, B. cereus, and Kitasatospora viridis, were inhibited by addition of rice husk biochar. All the biochars greatly supported the growth of B. mucilaginosus but inhibited that of K. viridis. More importantly, different strains exhibited discrepant growth response towards the same biochar sample, even when strains belong to the same species, suggesting that the effect of biochar on bacteria growth is strain-specific. Corncob biochar showed the strongest adsorption on B. thuringiensis but the greatest growth promotion was observed in B. mucilaginosus, indicating that the porous structure of biochar is not the sole factor that influences cell growth. Due to the possible stimulation or inhibition of water-soluble compounds existing in biochar, the growth variation of tested strains decreased or increased correspondingly when the washed biochar was applied, indicating that water-soluble compounds in fresh biochar play an important role in cell growth and such effect is also strain-dependent. Biochar application could also enhance potassium-/phosphate-solubilizing activities through promoting bacterial growth. All these results suggested that biochar might influence bacterial growth under different mechanisms. Our findings should be valuable for an in-depth understanding of the potential mechanism of soil bacteria changes following biochar incorporation and for biochar application in agriculture. Full article

β-1,3-Glucanase is considered as a useful enzymatic tool for β-1,3-glucan degradation to produce (1→3)-linked β-glucan oligosaccharides with pharmacological activity properties. To validly isolate β-1,3-glucanase-producing microorganisms, the soil of Wolfiporia extensa, considered an environment rich in β-1,3-glucan-degrading microorganisms, was subjected to high throughput sequencing. The results demonstrated that the genera Streptomyces (1.90%) and Arthrobacter (0.78%) belonging to the order Actinomycetales (8.64%) in the phylum Actinobacteria (18.64%) were observed in soil for P. cocos cultivation (FTL₁). Actinomycetes were considered as the candidates for isolation of glucan-degrading microorganisms. Out of 58 isolates, only 11 exhibited β-1,3-glucan-degrading activity. The isolate SYBCQL belonging to the genus Kitasatospora with β-1,3-glucan-degrading activity was found and reported for the first time and the isolate SYBC17 displayed the highest yield (1.02 U/mg) among the isolates. To check the β-1,3-glucanase contribution to β-1,3-glucan-degrading activity, two genes, 17-W and 17-Q, encoding β-1,3-glucanase in SYBC17 and one gene QLK1 in SYBCQL were cloned and expressed for verification at the molecular level. Our findings collectively showed that the isolates able to secrete β-1,3-glucanase could be obtained with the assistance of high-throughput sequencing and genes expression analysis. These methods provided technical support for isolating β-1,3-glucanase-producing microorganisms. Full article