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Panax notoginseng (Araliaceae) is an important ginseng herb with various health benefits and a history of cultivation in southwestern China over 400 years. In recent years P. notoginseng has faced serious continuous-cropping obstacles due to its large-scale cultivation. In this study, we aim to explore the allelochemicals of P. notoginseng and their interactions with various plants and rhizosphere microorganisms. The chemical constituents of the soil cultivated with 3-year-old P. notoginseng were studied by column chromatography, spectroscopic and GC-MS analyses. We identified 13 volatile components and isolated six triterpenes (1–4, 6–7) and one anthraquinone (5). Compounds 1–7 were tested for their effects on seed germination and root elongation in P. notoginseng, corn, wheat, turnip, water spinach and Arabidopsis thaliana. We also examined the effect of compounds 1–7 on the growth of ten rhizosphere microorganisms of P. notoginseng. At a concentration of 1.0 μg mL−1, compounds 3 and 5–7 caused the death of P. notoginseng root cells and compounds 2, 6 and 7 induced the death of root cells of A. thaliana. Compounds 1–5 and 7 inhibited elongation of A. thaliana root tip cells at a concentration of 10.0 μg mL−1. Moreover, at a concentration of 0.1 mg mL−1, compounds 3, 4, 6 and 7 inhibited the growth of probiotics and promoted the growth of pathogens of P. notoginseng. These results suggest that these isolated ursane-type triterpenoid acids and anthraquinone are potential allelochemicals that contribute to continuous-cropping obstacles of P. notoginseng.

Cephalotrichum microsporum is a fungus isolated from the rhizosphere soil of Panax notoginseng. Four secondary metabolites (three new and one known α-furanones) of this fungus cultivated on a sterilized moistened-rice medium were isolated using an EtOAc extract. The structures of these compounds were determined by extensive spectroscopic data analysis using 1D- and 2D-NMR, ECD, and HRESIMS. In the antibacterial bioassay, compounds 2 and 3 displayed moderate inhibitory effects on S. aureus and B. subtilis with an inhibition rate of more than 50% at a concentration of 50.0 μg/mL. Additionally, compounds 1 ‒ 4 displayed weak antibacterial effects on MR Staphylococcus aureus.

Inthomycins belong to a growing family of oxazole-containing polyketides and exhibit a broad spectrum of anti-oomycete and herbicidal activities. In this study, we purified inthomycins A and B from the metabolites of Streptomyces sp. strain SYP-A7193 and determined their chemical structures. Genome sequencing, comparative genomic analysis, and gene disruption of Streptomyces sp. SYP-A7193 showed that the inthomycin biosynthetic gene cluster (itm) belonged to the hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) system. Functional domain comparison and disruption/complementation experiments of itm12 resulted in the complete loss of inthomycins A and B and the subsequent restoration of their production, confirming that itm12 encodes a discrete acyltransferase (AT), and hence, itm was considered to belong to the trans-AT type I PKS system. Moreover, the disruption/complementation experiments of itm15 also resulted in the loss and restoration of inthomycin A and B formation. Further gene cloning, expression, purification, and activity verification of itm15 revealed that Itm15 is a cyclodehydratase that catalyzes a straight-chain dehydration reaction to form an oxazole ring for the biosynthesis of inthomycins A and B. Thus, we discovered a novel enzyme that catalyzes oxazole ring formation and elucidated the complete biosynthetic pathway of inthomycins. IMPORTANCEStreptomyces species produce numerous secondary metabolites with diverse structures and pharmacological activities that are beneficial for human health and have several applications in agriculture. In this study, hybrid nonribosomal peptide synthetase/polyketide synthase metabolites inthomycins A and B were isolated from after fermenting Streptomyces sp. SYP-A7193. Genome sequencing, gene disruption, gene complementation, heterologous expression, and activity assay revealed that the biosynthesis gene assembly line of inthomycins A and B was a 95.3-kb trans-AT type I PKS system in the strain SYP-A7193. More importantly, Itm15, a cyclodehydratase, was identified to be an oxazole ring formation enzyme required for the biosynthesis of inthomycins A and B; it is significant to discover this catalyzation reaction in the PKS/NRPS system in the field of microbiology. Our findings could provide further insights into the diversity of trans-AT type I PKS systems and the mechanism of oxazole cyclization involved in the biosynthesis of natural products.

Background Streptomycetes from the rhizospheric soils are a rich resource of novel secondary metabolites with various biological activities. However, there is still little information related to the isolation, antimicrobial activity and biosynthetic potential for polyketide and non-ribosomal peptide discovery associated with the rhizospheric streptomycetes of Panax notoginseng. Thus, the aims of the present study are to (i) identify culturable streptomycetes from the rhizospheric soil of P. notoginseng by 16S rRNA gene, (ii) evaluate the antimicrobial activities of isolates and analyze the biosynthetic gene encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) of isolates, (iii) detect the bioactive secondary metabolites from selected streptomycetes, (iv) study the influence of the selected isolate on the growth of P. notoginseng in the continuous cropping field. This study would provide a preliminary basis for the further discovery of the secondary metabolites from streptomycetes isolated from the rhizospheric soil of P. notoginseng and their further utilization for biocontrol of plants. Results A total of 42 strains representing 42 species of the genus Streptomyces were isolated from 12 rhizospheric soil samples in the cultivation field of P. notoginseng and were analyzed by 16S rRNA gene sequencing. Overall, 40 crude cell extracts out of 42 under two culture conditions showed antibacterial and antifungal activities. Also, the presence of biosynthesis genes encoding type I and II polyketide synthase (PKS I and PKS II) and nonribosomal peptide synthetases (NRPSs) in 42 strains were established. Based on characteristic chemical profiles screening by High Performance Liquid Chromatography-Diode Array Detector (HPLC-DAD), the secondary metabolite profiles of strain SYP-A7257 were evaluated by High Performance Liquid Chromatography-High Resolution Mass Spectrometry (HPLC-HRMS). Finally, four compounds actinomycin X2 (F1), fungichromin (F2), thailandin B (F7) and antifungalmycin (F8) were isolated from strain SYP-A7257 by using chromatography techniques, UV, HR-ESI-MS and NMR, and their antimicrobial activities against the test bacteria and fungus were also evaluated. In the farm experiments, Streptomyces sp. SYP-A7257 showed healthy growth promotion and survival rate improvement of P. notoginseng in the continuous cropping field. Conclusions We demonstrated the P. notoginseng rhizospheric soil-derived Streptomyces spp. distribution and diversity with respect to their metabolic potential for polyketides and non-ribosomal peptides, as well as the presence of biosynthesis genes PKS I, PKS II and NRPSs. Our results showed that cultivatable Streptomyces isolates from the rhizospheric soils of P. notoginseng have the ability to produce bioactive secondary metabolites. The farm experiments suggested that the rhizospheric soil Streptomyces sp. SYP-A7257 may be a potential biological control agent for healthy growth promotion and survival rate improvement of P. notoginseng in the continuous cropping field.

Two new compounds chetoseminudin F (1) and G (2) together with eleven known compounds were isolated from the solid fermentation products of the endophytic fungus Chaetomium sp. SYP-F7950. The structures of the isolated compounds were elucidated by extensive spectroscopic analyses, including 1D and 2D NMR, and HRFABMS experiments. The absolute configurations of chetoseminudin F (1) and G (2) were determined by comparing the electronic circular dichroism (ECD) spectrum with those of the reported references. A plausible biogenetic pathway for compounds 1–6 and 9–13 was proposed. These isolates were also evaluated for their antimicrobial and antitumor activity, revealing that chetoseminudin F (1) displayed more potent cytotoxicity against MDA-MB-231 cells with an IC50 value of 26.49 μmol L−1 more than the common chemotherapeutic agent (paclitaxel). In antimicrobial assay, compounds 6, 9, 11 and 12 had strong antibacterial activity against Staphylococcus aureus, Bacillus subtilis, Enterococcus faecium and antifungal activity against Candida albicans with minimum inhibitory concentration (MIC) values ranging from 0.12 to 9.6 μg mL−1; meanwhile compounds 6, 8, 9 and 12 exhibited strong cytotoxicity with IC50 values of 2.75–8.68 μmol L−1 against tumor cell lines A549 and MDA-MB-231. In addition, morphological observation showed that treatment with compounds 6, 9 and 12 increased the mean length of B. subtilis by 1.6 to 1.8-fold. In silico molecular docking was applied to study the binding interactions between the compounds and the active sites of filamentous temperature-sensitive protein Z (FtsZ) from B. subtilis. Compounds 6, 9 and 12 displayed the low binding energies, strong H-bond interactions with FtsZ. On the basis of the antimicrobial activities, cellular phenotype observation and docking studies, compounds 6, 9 and 12 are considered to be a promising antimicrobial inhibitor of FtsZ.

A total of 180 fungal isolates, belonging to 20 genera and 47 species, were obtained from the roots, stems and leaves of Panax notoginseng. One isolate, the endophytic fungus Penicillium janthinellum SYPF 7899, displayed the strongest antibacterial activity and was studied for its production of secondary metabolites. In total, three new compounds, including rotational isomers 1a, 1b and 2 were isolated from the solid cultures of P. janthinellum, as well as eight known compounds (3−10). These structures were determined on the basis of 1D, 2D NMR and electronic circular dichroism (ECD) spectroscopic analyses as well as theoretical calculations. Compound 1 exhibited significant inhibitory activities against Bacillus subtilis and Staphylococcus aureus with MIC values of 15 and 18 μg/ml, respectively. The other compounds showed moderate or weak activities. In addition, morphological observation showed the rod-shaped cells of B. subtilis growing into long filaments, which reached 1.5- to 2-fold of the length of the original cells after treatment with compound 1. The coccoid cells of S. aureus exhibited a similar response and swelled to a 2-fold volume after treatment with compound 1. In silico molecular docking was explored to study the binding interactions between the compounds and the active sites of filamentous temperature-sensitive protein Z (FtsZ) from B. subtilis and S. aureus. Compound 1a, 1b and 2 showed high binding energies, strong H-bond interactions and hydrophobic interactions with FtsZ. Based on the antimicrobial activities, cellular phenotype observation and docking studies, compound 1 is considered to be a promising antimicrobial inhibitor of FtsZ.

An endophytic strain (designated as strain SYPF 8335T) was isolated from a root of Panax notoginseng in Wenshan district, Yunnan province of China. Strain SYPF 8335T grew very slowly and formed white colonies. Phylogenetic analysis of four loci indicated that strain SYPF 8335T was placed in the Drechmeria clade with Drechmeria campanulata as its closest phylogenetic neighbour. The nucleotide differences between strain SYPF 8335T and D. campanulata are 30 substitutions in the internal transcriber region region. A key morphological feature that differentiates the two fungi is that D. campanulata produces campanulate conidia. Combined with the morphology and molecular analyses, a new species named Drechmeria panacis sp. nov., is proposed.

A novel 1(2), 2(18)-diseco indole diterpenoid, drechmerin H (1), was isolated from the fermentation broth of Drechmeria sp. together with a new indole diterpenoid, 2′-epi terpendole A (3), and a known analogue, terpendole A (2). Their structures were determined by HRESIMS, 1D and 2D NMR, ECD, and X-ray single crystal diffraction analyses as well as quantum chemical calculation. The abosulte configuration of terpendole A (2) was determined for the first time. Compound 1 displayed the significant agonistic effect on pregnane X receptor (PXR) with EC50 value of 134.91 ± 2.01 nM, and its interaction with PXR was investigated by molecular docking. Meantime, a plausible biosynthetic pathway for compounds 1–3 is also discussed in the present work.

A strain (SYPF 7183T) was isolated from rhizosphere soil of Panax notoginseng in southwest China. Phylogenetic analyses indicated that strain SYPF 7183T was distinct from the other Absidia species with well-supported values. Strain SYPF 7183T produced spherical or subpyriform sporangia and short cylindrical sporangiospores. The azygospores were globose to oval. Based on morphological and phylogenetic evidence, the novel strain Absidia panacisoli sp. nov. is proposed.

A total of 58 fungal isolates, belonging to 24 genera, were obtained from the leaves, stems and roots of Ginkgo biloba L.. Among them, one endophytic fungal strain, Penicillium cataractum SYPF 7131, displayed the strongest antibacterial activity. Four new compounds (1-4) were isolated from the strain fermentation broth together with four known compounds (5-8). These structures were determined on the basis of 1D and 2D NMR and [Rh2(OCOCF3)4]-induced electronic circular dichroism (ECD) spectroscopic analyses. All the isolated compounds were screened for their in vitro antimicrobial activities. Compound 3 and 4 showed moderate inhibitory activity against Staphylococcus aureus. Compound 7 exhibited significant inhibitory activity against S. aureus with MIC value of 10 μg/mL. Further, the in silico molecular docking studies of the active compounds was used to explore the binding interactions with the active site of filamentous temperature-sensitive protein Z (FtsZ) from Staphylococcus aureus. The docking results revealed that compounds 3, 4 and 7 showed high binding energies, strong H-bond interactions and hydrophobic interactions with FtsZ from S. aureus validating the observed antimicrobial activity. Based on antimicrobial activities and docking studies, compounds 3, 4 and 7 were identified as promising antimicrobial lead molecules.

A Gram-stain-negative, strictly aerobic, yellow-coloured, motile by gliding and elongated rod-shaped bacterial strain, designated SYP-B1015T, was isolated from the rhizosphere of Artemisia annua L. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SYP-B1015T belonged to the genus Flavobacterium and had highest 16S rRNA gene sequence similarity to Flavobacterium compostarboris JCM 16527T (98.1 %) and Flavobacterium procerum JCM 30113T (97.2 %). The predominant respiratory quinone for the strain was MK-6, and the major cellular fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine as a major compound. The DNA G+C content of strain SYP-B1015T was 33.5 mol%. The DNA–DNA relatedness values between strain SYP-B1015T and F. compostarboris JCM 16527T and F. procerum JCM 30113T were 56.5±0.4 and 48.9±1.2 %, respectively. Combining the data from morphological, physiological, biochemical and chemotaxonomic characterizations presented in this study, strain SYP-B1015T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium artemisiae sp. nov. is proposed. The type strain is SYP-B1015T (=CGMCC 1.16115T=KCTC 62025T).

A novel yellow pigmented, Gram-positive, aerobic and heavy metal biosorptive bacterium designated SYP-B2667T was isolated from rhizosphere soil of Epilobium hirsutum L. in Tongren, Guizhou province, China. Based on 16S rRNA gene sequence analyses, it was shown that strain SYP-B2667T represents a novel species in the genus Leucobacter, with Leucobacter chromiireducens subsp. solipictus JCM 15573T as a close phylogenetic neighbour (sequence similarity of 98.2%). Chemotaxonomic characteristics also supported the affiliation to the genus Leucobacter. Strain SYP-B2667T was determined to have a DNA G+C content of 66.6 mol%; 2,4-diaminobutyric acid in the cell wall peptidoglycan amino acids; MK-11 as predominant menaquinone; an abundance of anteiso-C15:0 and anteiso-C17:0 fatty acids; and polar lipids including diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified phospholipids. The DNA–DNA hybridization value between strain SYP-B2667T and L. chromiireducens subsp. solipictus JCM 15573T was 19.7 ± 2.8%. Based on these phylogenetic and phenotypic results, it can be concluded that strain SYP-B2667T represents a novel species, for which the name Leucobacter epilobiisoli sp. nov. is proposed. The type strain is SYP-B2667T (=DSM 105145T=CPCC 204976T). This strain can tolerate and adsorb five heavy metals and so may have potential to facilitate heavy metal removal and bioremediation.

A Gram-stain-positive, rod-shaped, motile bacterium designated as SYP-B691T was isolated from rhizospheric soil of Panax notoginseng. Phylogenetic analysis indicated that SYP-B691T clearly represented a member of the genus Bacillus and showed 16S rRNA gene similarity lower than 97.0 % with the type strains of species of the genus Bacillus , which indicates that it should be considered as a candidate novel species within this genus. The optimum growth of the strain was found to occur at 37 °C and pH 7.0–9.0. The genomic DNA G+C content was determined to be 45.2 mol%. It contained meso-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. MK-7 was the only menaquinone identified. The major cellular fatty acids of SYP-B691T were identified as iso-C15 : 0 and anteiso-C15 : 0. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, SYP-B691T merits recognition as a representative of a novel species of the genus Bacillus , for which the name Bacillus notoginsengisoli sp. nov. is proposed, with SYP-B691T(=DSM 29196T=JCM 30743T) as the type strain.

In this Letter, the Darboux transformation is first applied to the defocusing Sasa–Satsuma equation which describes the propagation dynamics of ultrashort light pulses in the normal dispersion regime of optical fibers. The N -fold iterative transformation is expressed in terms of the determinants. This transformation enables us to construct explicit analytical dark soliton solutions from non-vanishing background. In illustration, the single-dark soliton solution is presented from the once-iterated formula.

A total amount of 116 fungal strains, belonging to 30 genera, were acquired from the rhizosphere soil and plant of Galinsoga parviflora. A strain SYPF 7336, isolated from the rhizospheric soil, was identified as Seltsamia galinsogisoli sp. nov., by morphological and molecular analyses, which displayed high antibacterial activity. In order to study the secondary metabolites of Seltsamia galinsogisoli sp. nov., nine compounds were successfully seperated from the strain fermentation broth, including two new compounds and seven known compounds. Their structures were elucidated based on spectral analysis including 1D and 2D NMR. All the seperated compounds were evaluated for their antimicrobial activities. Compounds 2, 5 and 1 displayed antimicrobial activities against Staphylococcus aureus with MIC values of 25, 32 and 75 μg/mL, respectively. Moreover, morphological observation showed the coccoid cells of S. aureus to be swollen to a volume of 1.4 to 1.7-fold after treatment with compounds 1, 2 and 5, respectively. Molecular docking was carried out to investigate interactions of filamentous temperature-sensitive protein Z (FtsZ) with compounds 1, 2 and 5.

Five new derivatives of macrolide antibiotic Brefeldin A (BFA, 6), named as Brefeldin E1–E5 (1–5), along with Brefeldin A 7-O-acetate (7), mycotoxins (8–9) and mangrovamides A (10) were produced by an endophytic fungus, Penicillium sp., which was isolated from the healthy root of Panax notoginseng. The structures of 1–5 were established on the basis of their spectroscopic data, while the absolute configurations were assigned using a modified Mosher's method. All compounds were evaluated for their cytotoxic, antiviral and antimicrobial activities. Compounds 1–5 and 8–10 displayed low or moderate cytotoxicity against a panel of cancer cell lines. Compounds 1, 2, 4, 5, and 8–10 showed moderate antimicrobial activity. Compound 6 showed strong anticancer and antiviral properties. Additionally, it demonstrated broad-spectrum activity against human pathogenic bacteria and fungal pathogens that can cause root-rot disease in Panax notoginseng, including Escherichia coli, Staphylococcus aureus, Bacillus cereus, Klebsiella pneumonia, Candida albicans, Fusarium solani, Cylindrocarpon didynum and Alternaria panax. Compound 7, which could be mediated by 6 through the acetylation at the 7-hydroxyl, showed similar bioactivities to compound 6. Further studies of the cellular mechanism of compounds 6 and 7 showed that they arrested HepG2 cells at the S phase. Due to the similarities in the basic carbon skeleton and the chemical construction correlations between compounds 1–7, the plausible biosynthetic pathway of the BFA series of compounds has been proposed and their structure–activity relationships are also discussed.

An endophytic strain (designated as SYPF 7195T) was isolated from a branch of a ginkgo tree in Liaoning province of China. Strain SYPF 7195T was characterized by its grey to greyish-green aerial mycelium, velvety to floccose surface and swelling near the septa. Phylogenetic analyses, which were inferred from the internal transcribed spacer (ITS) and partial sequences of the LSU and SSU of the rDNA and translation elongation factor 1-alpha (TEF1), showed that strain SYPF 7195T belonged to the genus Pseudochaetosphaeronema, and was distinct from all other species with high bootstrap-supported values (92 %). Strain SYPF 7195T constitutes a separate evolutionary clade with Pseudochaetosphaeronema larense and Pseudochaetosphaeronema martinelli, with P. martinelli as its closest phylogenetic neighbour. The nucleotide differences between strain SYPF 7195T and P. martinelli were 71 substitutions in the ITS region. Strain SYPF 7195Tcould also be distinguished from P. martinelli by a number of physiological characteristics. Combined with morphology and molecular analyses, strain SYPF 7195T merits recognition as a representative of a novel species of the genus Pseudochaetosphaeronema, for which the name Pseudochaetosphaeronema ginkgonis sp. nov. is proposed. The type strain is CBS 140953T (=CGMCC 3.17865T=SYPF 7195T). The Mycobank number is MB 816567.

A Gram-staining-negative, yellow-pigmented strain, designated SYP-B804T, was isolated from the rhizosphere of Panax notoginseng. The strain was rod-shaped with a single polar flagellum. The optimum temperature and pH required for growth of the strain were 28-32 °C and pH 7-8, respectively. 16S rRNA gene sequence analysis indicated that strain SYP-B804T showed highest 16S rRNA gene sequence similarity with Luteimonas mephitis DSM 12574T (98.0 %). However, the DNA-DNA relatedness value between them (38.1 ± 0.6 %) was less than the threshold value for the delineation of genomic species. Ubiquinone-8 (Q-8) was the predominant quinone. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 71 %. On the basis of phenotypic, chemotaxonomic and molecular characteristics, strain SYP-B804T merits recognition as a representative of a novel species of the genus Luteimonas, for which the name Luteimonas notoginsengisoli sp. nov. is proposed, with SYP-B804T ( = KCTC 42211T = JCM 30329T) as the type strain.

(+) Benzomalvins E (1) and (-) Benzomalvins E (2), a pair of epimeric derivatives, together with three known benzomalvins (3–5), were isolated from solid cultures of a interrhizospheric fungus Penicillium sp. SYPF 8411. The planar structure of (+) Benzomalvins E (1) has been previously reported. While, the absolute configuration of compound 1 was established by X-ray crystallographic analysis for the first time. The planar structure of the new compound 2 were elucidated by detailed interpretation of their HR ESI-TOF MS and NMR spectroscopic data. The absolute configuration of compound 2 was established by Rh2(OCOCF3)4-induced CD spectral data and the electronic circular dichroic (ECD) method. Furthermore, the epimerization induced by pH, temperature and H2O was revealed. Benzomalvins (1–3, 5), a type of indoximod, enhanced the cytotoxic capability of 5-fluorouracil against A549.

Two new compounds, (7R, 2E, 5E)-3,5,7-trimethyl-2,5-octadienedioic-8-methyl ester (1) and neovasipyridone G (3), together with a new natural product compound (7R,2E,5E)-3,5,7-trimethyl-2,5-octadienedioic acid (2), and six known compounds (4–9) were isolated from Penicillium sp. SYPF7381. Their structures were elucidated on the basis of extensive spectroscopic analysis, and the absolute configurations of compounds 1 and 2 were determined by optical rotation. The absolute configuration of compound 3 was determined by means of electronic circular dichroism (ECD) calculation. In addition, the in vitro anti-inflammatory activities of all compounds were assayed in RAW 264.7 cells by assessing LPS-induced NO production. Furthermore, the structure-antiinflammation activity relationships for these isolated compounds were summarized based on the experimental as well as the docking results.

Cephalotrichum microsporum (SYP-F 7763) was a fungus isolated from the rhizosphere soil of traditional Chinese medicine Panax notoginseng. The EtOAc extract of Cephalotrichum microsporum cultivated on sterilized moistened-rice medium was separated by various chromatographic techniques, which yielded 11 metabolites (1–11) of this fungus. On the basis of the widely spectroscopic data, the chemical structures of isolated metabolites were determined, most of which were α-pyrones, including 5 compounds (4–7, and 10) unreported. In the anti-bacterial bioassay, compound 1 displayed significant inhibitory effects on three pathogenic bacteria, MR S. aureus, S. aureus, and B. cereus. α-Pyrones 2, 3, and 5–7 also displayed moderate inhibitory effects on MR S. aureus, S. aureus, and B. subtilis, which could be the major anti-bacterial constituents of Cephalotrichum microsporum. Additionally, compounds 1, 4, and 5 displayed significant cytotoxicity on five human cancer cell lines, with the IC50 values

A Gram-negative, facultatively anaerobic, non-motile, nonspore- forming, coccoid or rod-shaped and creamy-pigmented bacterium, designated SYP-B2100T, was isolated from the rhizospheric soil of Codonopsis clematidea in the Xinjiang Uygur Autonomous Region, China. The optimal growth occurred at 28°C, pH 5.0, in the absence of NaCl. The cells tested positive in catalase and methyl red tests but negative in oxidase, urease, gelatinase, milk coagulation, and peptonisation, H2S production, nitrate reduction, and Voges-Proskauer tests. The major isoprenoid quinone was ubiquinone-8 (Q-8). The major cellular fatty acids were C16:0 and summed feature 8. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The 16S rRNA gene sequence of strain SYP-B2100T was the most similar to that of Rahnella inusitata DSM 30078T (96.9%) within the family Enterobacteriaceae. The genomic DNA G + C content of strain SYP-B2100T was 50.3 mol%. The combined data from the phylogenetic, morphological, physiological, biochemical, and chemotaxonomic analyses presented in this study support the conclusion that strain SYP-B2100T represents a novel species of a new genus, for which the name Edaphovirga cremea gen. nov., sp. nov. is proposed; the type strain is SYPB2100T (= CGMCC 1.5857T = DSM 105170T = KCTC 62024T).

An endophytic strain (designated as strain SYPF 8337T) was isolated from the root of 3-year-old Panax notoginseng in Yunnan province of China. Strain SYPF 8337T grew slowly and formed pale brown to brown colonies. Phylogenetic analyses indicated that strain SYPF 8337T was placed in the Verruconis clade. Different from other Verruconis species, strain SYPF 8337T produced four-cell conidia. Furthermore, strain SYPF 8337T is the first fungus isolated as an endophyte of P. notoginseng in the genus Verruconis. Combined with the morphology and molecular analyses, a new species named Verruconis panacis sp. nov. is proposed.

Background 2-Keto-l-gulonic acid (2-KGA), the precursor of vitamin C, is currently produced by two-step fermentation. In the second step, l-sorbose is transformed into 2-KGA by the symbiosis system composed of Ketogulonicigenium vulgare and Bacillus megaterium. Due to the different nutrient requirements and the uncertain ratio of the two strains, the symbiosis system significantly limits strain improvement and fermentation optimization. Results In this study, Ketogulonicigenium robustum SPU_B003 was reported for its capability to grow well independently and to produce more 2-KGA than that of K. vulgare in a mono-culture system. The complete genome of K. robustum SPU_B003 was sequenced, and the metabolic characteristics were analyzed. Compared to the four reported K. vulgare genomes, K. robustum SPU_B003 contained more tRNAs, rRNAs, NAD and NADP biosynthetic genes, as well as regulation- and cell signaling-related genes. Moreover, the amino acid biosynthesis pathways were more complete. Two species-specific internal promoters, P1 (orf_01408 promoter) and P2 (orf_02221 promoter), were predicted and validated by detecting their initiation activity. To efficiently produce 2-KGA with decreased CO2 release, an innovative acetyl-CoA biosynthetic pathway (XFP-PTA pathway) was introduced into K. robustum SPU_B003 by expressing heterologous phosphoketolase (xfp) and phosphotransacetylase (pta) initiated by internal promoters. After gene optimization, the recombinant strain K. robustum/pBBR-P1_xfp2502-P2_pta2145 enhanced acetyl-CoA approximately 2.4-fold and increased 2-KGA production by 22.27% compared to the control strain K. robustum/pBBR1MCS-2. Accordingly, the transcriptional level of the 6-phosphogluconate dehydrogenase (pgd) and pyruvate dehydrogenase genes (pdh) decreased by 24.33 ± 6.67 and 8.67 ± 5.51%, respectively. The key genes responsible for 2-KGA biosynthesis, sorbose dehydrogenase gene (sdh) and sorbosone dehydrogenase gene (sndh), were up-regulated to different degrees in the recombinant strain. Conclusions The genome-based functional analysis of K. robustum SPU_B003 provided a new understanding of the specific metabolic characteristics. The new XFP-PTA pathway was an efficient route to enhance acetyl-CoA levels and to therefore promote 2-KGA production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0932-9) contains supplementary material, which is available to authorized users.

Two novel bacterial strains, designated SYP-B540(T) and SYP-B556, were isolated from rhizospheric soil of Panax notoginseng located at Yunnan Province, China. Both strains were Gram-staining negative, aerobic, non-motile, elongated rod shaped and yellow coloured. They grew optimally at 28 °C and pH 7.0. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but lower than 97.6 % to the other known species of the genus Flavobacterium. The predominant respiratory quinone for the two strains was MK-6, and the major fatty acids were iso-C15:0 and summed Feature 3 (comprising 16:1 ω7c and/or 16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine, two unidentified polar lipids and three unidentified amino-phospholipids. The DNA G+C contents of strains SYP-B540(T) and SYP-B556 were 33.3 and 32.7 mol%, respectively. In addition, the DNA-DNA hybridization values of strains SYP-B540(T) and SYP-B556 to their closest phylogenetic neighbors were significantly lower than 70 %. On the basis of the polyphasic taxonomy studies, strains SYP-B540(T) and SYP-B556 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium notoginsengisoli sp. nov. is proposed. The type strain is SYP-B540(T) (=KCTC 32505(T) = NBRC 110012(T) = BCRC 80724(T)).

A search for cytotoxic agents from cultures of the Penicillium sp., isolated from the rhizosphere soil of Pulsatilla chinensis, led to the isolation of four new hybrid polyketide-terpenoid metabolites (1–4), together with fourteen known compounds (5–18). Using a bioassay-guided fractionation approach, eighteen compounds were obtained from the ethyl acetate extract of this fungus. Structure elucidation was achieved by extensive analysis of spectroscopic data (1D/2D NMR, HRESIMS and IR). The absolute configurations of compounds 1–4 were determined by means of electronic circular dichroism (ECD) calculation. Compounds 1–4, 7–9, 11, 12, 14 and 17 were tested for their cytotoxicity against HL-60, THP-1 and Caco2 cell lines. Compound 1 showed potent cytotoxic capability against HL-60, THP-1 and Caco2 cell with IC50 values of 3.4 μM, 4.3 μM, 10.5 μM, and compound 2 showed significant inhibiting activities against HL-60 cell line and THP-1 cell line (IC50 = 7.9 μM, 11.3 μM, respectively), using 5-fluorouracil as the positive drug with IC50 values of 6.4 μM, 4.4 μM, 56.6 μM for HL-60, THP-1 and Caco2 cells, respectively. And compound 1 showed antibacterial activity toward Bacillus cereus (IC50 = 49 μg/mL, IC90 = 111 μg/mL) and Bacillus subtilis (IC50 = 10 μg/mL, IC90 = 85 μg/mL).

Five new 12-membered resorcylic acid lactone derivatives, penicimenolides A-E (1–5), one new ring-opened resorcylic acid lactone derivative penicimenolide F (6) and six known biogenetically related derivatives (7–12) were isolated from the culture broth of a strain of Penicillium sp. (NO. SYP-F-7919), a fungus obtained from the rhizosphere soil of Panax notoginseng collected from the Yunnan province of China. Their structures were elucidated by extensive NMR analyses, a modified Mosher’s method, chemical derivatization and single crystal X-ray diffraction analysis. Compounds 2–4 exhibited potent cytotoxicity against the U937 and MCF-7 tumour cell lines and showed moderate cytotoxic activity against the SH-SY5Y and SW480 tumour cell lines. The substitution of an acetyloxy or 2-hydroxypropionyloxy group at C-7 significantly increased the cytotoxic activity of the resorcylic acid lactone derivatives. Subsequently, the possible mechanism of compound 2 against MCF-7 cells was preliminarily investigated by in silico analysis and experimental validation, indicating compound 2 may act as a potential MEK/ERK inhibitor. Moreover, proteomics analysis was performed to explore compound 2-regulated concrete mechanism underlying MEK/ERK pathway, which is still need further study in the future. In addition, compounds 2–4 and 7 exhibited a significant inhibitory effect on NO production induced by LPS.

In this study, a novel Lactococcus garvieae B301 was isolated from the intestinal tract of a healthy piglet. L. garvieae B301 was tolerant to acid pH, simulated gastric and small intestinal transit juices, indicating that it was capable of surviving in the gastrointestinal tract. L. garvieae B301 was safe and beneficial to broilers, as broiler chickens supplemented with L. garvieae B301 had lower diarrhoea incidence and mortality than the Control. Moreover, supplementation of broiler diets with L. garvieae B301 resulted in an increase in body weight and the number of caecum lactic acid bacteria and Bifidobacterium spp., and decrease in feed-to-gain ratio and the number of caecum coliforms. It also had a positive effect on the thymus index and bursa of Fabricius index and enhanced serum levels of immune globulins. All these results showed that L. garvieae B301 could enhance the growth performance of broiler chickens and improve their health. Thus, L. garvieae B301 could be a promising feed additive for broiler chickens.

A Gram-positive, aerobic, non-motile and pale yellow colour actinobacterial strain, designated SYP-B575(T), was isolated from rhizosphere soil of Panax notoginseng. The optimal growth of the strain was found to occur at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis indicated that strain SYP-B575(T) clearly belongs to the genus Sinomonas and should be considered as a candidate of novel species within this genus. The 16S rRNA gene sequence similarities between strain SYP-B575(T) and the other Sinomonas type strains ranged from 97.3 to 96.0%. The predominant isoprenoid quinone was identified as MK-9(H2) and the major fatty acids were identified as anteiso-C(15:0) and anteiso-C(17:0). The polar lipids were found to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and glycolipids. The major cell-wall amino acids were identified as Lys, Ala, Glu, Gly and Ser. The whole-cell sugars were identified as mannose, ribose, rhamnose, glucose and galactose. The G+C content of the genomic DNA was determined to be 66.6 mol%. The DNA-DNA relatedness values between SYP-B575(T) and its closest phylogenetic neighbours were lower than 35.5%. On the basis of this polyphasic taxonomic study, strain SYP-B575(T) represents a novel species of the genus Sinomonas, for which the name Sinomonas notoginsengisoli sp. nov. is proposed. The type strain is SYP-B575(T) (=DSM 27685(T) = KCTC 29237(T)).