Phoma Sp Research Articles

The complete mitogenome of Alternaria tenuissima (Kunze) Wiltshire 1933 (Pleosporaceae), a fungus causing apple leaf blotch disease

Alternaria tenuissima (Kunze) Wiltshire 1933 is a plant pathogenic fungus mainly causing leaf blotch disease. Here, we de novo assembled mitochondrial genome of A. tenuissima isolate AT-1224. The total mitogenome size is 57,475 bp with 29.00% G + C content. The genome contained 12 coding genes and 15 hypothetical proteins, 34 transfer RNA (tRNA) genes and 2 ribosomal RNA (rRNA). There are 227 SSR repeats, range from 2 to 4 base pairs, most five repeats were AT (144), AAT (54), AG (33), AC (13) and AAG (5). The results also found 13 tandem repeats (>100 bp), the largest repeat were forward 2 times located from 13,405 to 20,024 bp and 25,549 to 32,168 bp. Phylogenetic analysis based on 17 species complete mitogenomes indicated that A. tenuissima mitogenome was closest to 2 species, A. solani and A. alternata, sister clade to 6 species, representing Curvularia clavate, Exserohilum rostratum, Exserohilum turcicum, Bipolaris cookie, Bipolaris oryzae and Bipolaris sorokiniana. Further analysis among common fungus in local apple orchards using mitochondrial protein-coding genes revealed A. tenuissima were closing to 2 Alternaria fungi and a fungus representing Phoma sp. These results provide a basic reference for identification and evolution studies of A. tenuissima on apple trees.

Molecular phylogenetic characterization of L-asparaginase-producing endophytic fungi inhabiting Prunus africana and Periploca linearifolia: Effect of incubation time and pH on enzyme production

The therapeutic use of L-asparaginase derived from bacterial sources has been constrained by various challenges, including toxicity and repression. This has prompted the exploration of alternative sources, particularly eukaryotic microorganisms like fungi, to enhance the safety and effectiveness of the L-asparaginase enzyme. This study aims to investigate the fungal endophytes inhabiting Periploca linearifolia and Prunus africana as a potential source of novel L-asparaginase. Additionally, the study seeks to examine the impact of incubation time and pH on L-asparaginase production. Standard surface sterilization techniques were used for isolation of endophytic fungi. Based on the research findings, 24 % of the fungal endophytes demonstrated a positive reaction for L-ASNase activity and were identified as Colletotrichum sydowii, Fusarium sporotrichioides, Fusarium solani, Cercospora canescens, Penicillium crustosum, Penicillium pancosmium, Phoma sp, Penicillium ubiquetum, septoria sp and Penicillium commune. A significant variation in the production of L-asparaginase based on the time of incubation and pH was observed. Most endophytic fungal isolates exhibit optimal enzyme activity on the 6th day of incubation. However, both Septoria sp and Colletotrichum sydowii recorded the highest L-asparaginase activity on the 9th day of incubation. Fusarium solani demonstrated peak activity of 12.4 ± 1.12 UI/mL on the 12th day of incubation. The optimal pH for L-asparaginase production by fungal endophytes was found to be between 5 and 6. The fungal endophytes isolated from medicinal plants have the potential to serve as sources of novel L-asparaginase. Furthermore, it is evident that fungal endophytes display considerable variation in L-asparaginase production, influenced by the duration of incubation and pH conditions.

Endophytic fungi from Cissus quadrangularis plant a promising source of bioactive compounds.

Cissus quadrangularis is a succulent, perennial plant belonging to the family Vitaceae typically found in Asia and Africa's tropical and subtropical forest zones. It is an ancient medicinal plant, containing phytosterols, polyphenols, flavonoids, carbohydrates, and ascorbic acid. Due to the presence of phytosterols it plays a crucial role in bone fracture healing. However, due to the limited resources of these medicinal plants there is a need to search for a reservoir of biologically active metabolites. This medicinal property of the plants therefore may be attributed to the endophytic fungi within the plant. This study includes isolation of endophytic fungi from C. quadrangularis and the characterization of fungal extracts. Three endophytes were isolated namely Colletotrichum gloeosporioides, Colletotrichum siamense and Phoma sp. The qualitative analysis of targeted metabolites from Cissus quadrangularis stem and fungal extracts of all the three endophytes showed the presence of phytosterols. Methanol extracts of endophytes and C. quadrangularis plant exhibit significant antioxidant and the radical scavenging activity because of the presence of β-carotene. The Ic50 value for stem and isolated endophytes was 5.748, 19.937, 7.00, and 6.493 respectively. This study will give further scope for studying the bone healing ability of phytosterol from the endophytic isolates of C. quadrangularis plant.

Identifying the fungal diseases of African Yam Bean (Sphenostylis stenocarpa) and their incidence in south-west Nigeria

The incidence of fungi infecting Sphenostylis stenocarpa ([Hochst ex. A. Rich.] Harms) commonly known as African yam bean (AYB) were surveyed in Oyo, Ondo, Ekiti, Osun, and Ogun states within SW Nigeria during the 2018 planting season. The common field symptoms across all sites were tiny spot, brown spot, leaf blight, brown spot with yellow halo, necrotic lesion on foliage, and brown spot on the pods. Of these 1005 isolations, 14 fungal species were commonly identified after their purification: Aspergillus sp, Botrytis sp, Colletotrichum gloeosporioides, Curvularia lunata, Trichoderma harzianum, Macrophomina phaseolina, Pestalotia sp, Phoma sp, Fusarium verticillioides, F. oxysporum, F. solani, Botryodiplodia theobromae, Choanephora curcubitarium and Nigrospora spp. based on morphological characteristics. Phoma sp and C. gleosporoides had highest frequency of occurrence 69.9% and 51.9% at early and mature stages, respectively. To conform to Koch's postulates, the pathogenicity of 15 exemplar strains of the most abundant fungal species were confirmed under greenhouse conditions. The identities of Colletotrichum sp., Aspergillus sp., Curvularia aeria, Macrophomina phaseolina, Didymella sp., Pestalopsis sp, Lasiodiplodia theobromae, F. solani and F. oxysporum were confirmed based on internal transcribed spacer (ITS) sequencing and comparisons with the Genbank database. AYB germplasm from curated seed banks and farmer donated landraces were grown at the same site in 2020 and identical fungi were isolated. Further, genotypes with reduced disease incidence were identified. This first study to reveal the diversity of fungi associated with AYB in SW Nigeria that could inform disease management practices.

Fungal polyketides produced by an endophytic fungus Phoma sp. associated with Gastrodia elata

Two novel fungal polyketides, phometides A (1) and B (2), together with four known compounds (3–6), were isolated from the endophytic fungus Phoma sp. YUD17001 obtained from Gastrodia elata Blume. The structures were elucidated based on spectroscopic analyses, X-ray crystal diffraction, and time-dependent density functional theory/electronic circular dichroism (TDDFT/ECD) calculations. Structurally, phometide A (1) represented the first example of C12 polyketide characterized by an unusual tetrahydrobenzofuran-3(2H)-one core with an α,β-unsaturated ketone functionality, while phometide B (2) was an unprecedented molecule containing a 2-pentylcycloheptan-1-one scaffold. In an antimicrobial activity assay, phometide A (1) exhibited significant inhibitory activity against Staphylococcus aureus with MIC value of 4 μg/mL. Phometide B (2) showed moderate antifungal activity against Candida albicans with an MIC value of 16 μg/mL. Furthermore, compounds 1 and 2 were evaluated for their acetylcholinesterase inhibitory and cytotoxic activities.

Draft genome sequence of the endophytic fungus Phoma sp. strain YAFEF320, isolated from Gerbera jamesonii.

Here, we report a draft genome sequence of endophytic fungus Phoma sp. strain YAFEF320, isolated from the roots of Gerbera jamesonii. The genome size of Phoma sp. YAFEF320 was 32,542,820 bp with 52.08% GC content. The genome resource will support future research into potential secondary metabolite diversity of this fungus.

Isolation and Characterization of Novel Huperzine-Producing Endophytic Fungi from Lycopodiaceae Species.

Huperzine A (HupA) is an important drug for treating Alzheimer's disease (AD) and is primarily extracted from the Huperzia serrata (Lycopodiaceae). Failures in the chemical synthesis of Hup and in vitro culture have put H. serrata in danger of extinction, and there is a need for an extensive investigation of Hup from alternative perspectives. The aim of this study is to identify endophytic fungi that produce high Hup or simultaneously produce many types of Hup and have high genetic stability derived from other Lycopodiaceae species as a source of materials for natural Hup production. In this work, Hup-producing endophytic fungi were isolated from three species: Lycopodium clavatum, Phlegmariurus squarrosus, and P. phlegmaria. Of these, L. clavatum and P. squarrosus were confirmed as novel sources of Hup-producing fungi. Based on morphological characteristics and nuclear ribosomal DNA ITS sequences, four endophytic fungi Colletotrichum siamense THG1-17, Epicoccum sorghinum THG01-18, Phoma sp. TKH3-2, and Phyllosticta sp. THG2-27 were firstly isolated from these Lycopodiaceae plants, which were capable of simultaneously producing both HupA and HupB, as evidenced by high-performance liquid chromatography analysis. The four strains showed stability in Hup yield over 50 generations of culture with an in vitro storage period of 3 months. These isolated fungi will provide a new source of materials for further research to develop drugs containing HupA as well as HupB for AD treatment in the future.

Biosynthesis of Phomactin Platelet Activating Factor AntagonistRequires a Two-Enzyme Cascade.

Phomactin diterpenoids possess a unique bicyclo[9.3.1]-pentadecane skeleton with multiple oxidative modifications, and are good platelet-activating factor (PAF) antagonists that can inhibit PAF-induced platelet aggregation. In this study, we identified the gene cluster (phm) responsible for the biosynthesis of phomactins from amarine fungus,Phoma sp. ATCC 74077. Despite the complexity of their structures, phomactin biosynthesis only requires two enzymes: a type I diterpene cyclase PhmA and a P450 monooxygenase PhmC. PhmA was found to catalyze the formation of the phomactatriene, while PhmC sequentially catalyzes the oxidation of multiple sites, leading to the generation of structurally diverse phomactins. The rearrangement mechanism of the diterpene scaffold was investigated through isotope labeling experiments. Additionally, we obtained the crystal complex of PhmA with its substrate-analogue FGGPP and elucidated the novel metal ion binding mode and enzymatic mechanism of PhmA through site-directed mutagenesis. This work provides the first insights into the biosynthesis of phomactins, laying the foundation for the efficient production of phomactin natural products using synthetic biology approaches.

Biosynthesis of Phomactin Platelet Activating Factor Antagonist Requires a Two‐Enzyme Cascade

AbstractPhomactin diterpenoids possess a unique bicyclo[9.3.1]pentadecane skeleton with multiple oxidative modifications, and are good platelet‐activating factor (PAF) antagonists that can inhibit PAF‐induced platelet aggregation. In this study, we identified the gene cluster (phm) responsible for the biosynthesis of phomactins from a marine fungus, Phoma sp. ATCC 74077. Despite the complexity of their structures, phomactin biosynthesis only requires two enzymes: a type I diterpene cyclase PhmA and a P450 monooxygenase PhmC. PhmA was found to catalyze the formation of the phomactatriene, while PhmC sequentially catalyzes the oxidation of multiple sites, leading to the generation of structurally diverse phomactins. The rearrangement mechanism of the diterpene scaffold was investigated through isotope labeling experiments. Additionally, we obtained the crystal complex of PhmA with its substrate analogue FGGPP and elucidated the novel metal‐ion‐binding mode and enzymatic mechanism of PhmA through site‐directed mutagenesis. This study provides the first insight into the biosynthesis of phomactins, laying the foundation for the efficient production of phomactin natural products using synthetic biology approaches.

Phomaketals A and B, pentacyclic meroterpenoids from a eupC overexpressed mutant strain of Phoma sp.

Phomaketals A (1) and B (2), two tropolonic meroterpenoids with the unprecedented pentacyclic skeletons, were isolated from the solid-substrate fermentation cultures of a eupC overexpressed mutant strain of the fungus Phoma sp., together with a biogenetically related secondary metabolite pughiinin B (3), and the known one noreupenifeldin B (4). The structures of 1–3 were elucidated primarily by nuclear magnetic resonance (NMR) experiments. The absolute configurations of 1 and 2 were assigned by electronic circular dichroism calculations and the calculated NMR with DP4+ analysis, while that of 3 was established by single-crystal X-ray diffraction analysis using Cu Kα radiation. Biogenetically, phomaketals A (1) and B (2) could be derived from the hypothetical tropolonic sesquiterpene intermediates neosetophomone B (6) and 9-R-neosetophomone B (6′), respectively, via different reactions cascades. Compound 1 showed antiproliferative effect only against the SUPB15 cells, with an 50% inhibitory concentration (IC50) value of 4.85 µmol/L, while the co-isolated known meroterpenoid 4 displayed potent effects against three tumor cell lines, SUPB15, EL4, and H9, showing IC50 values of 0.36–27.08 µmol/L.

Isolation and Chemical Structural Elucidation of Antibacterial Bioactive Compounds from Endophytic Fungal Strain Phoma sp. D1

Isolation and Chemical Structural Elucidation of Antibacterial Bioactive Compounds from Endophytic Fungal Strain Phoma sp. D1

Diversity, antibacterial activity and chemical analyses of gut-associated fungi isolated from the Crocothemis servilia.

Insect-associated fungi are a potentially rich source of novel natural products with antibacterial activity. Here, we investigated the community composition and phylogenetic diversity of gut-associated fungi of the dragonfly (Crocothemis Servilia) using a combination of culture-dependent and culture-independent methods. A total of 42 fungal isolates were obtained from the guts of the dragonfly, which belonged to four classes and thirteen different genera. Amplicon sequencing analyses revealed that the fungal communities were more diverse, and a total of 136 genera were identified and dominated by the genera Wojnowiciella and Phoma. The antibacterial bioassay showed that five fungal crude extracts of representative isolates have shown antibacterial activities. Among them, the extract of Phoma sp. QTH17 showed the best antibacterial activities against Escherichia coli, Micrococcus tetragenus, and Staphylococcus aureus with the disc diameter of inhibition zone diameter (IZD) of 6.50, 10.80, and 8.70 mm, respectively. Chemical analysis of Phoma sp. QTH17 led to the discovery of five known compounds, including ergosterol (1), 3-Chlorogentisyl alcohol (2), epoxydon (3), epoxydon 6-methylsalicylate ester (4) and mannitol (5). Among them, the compound 3 exhibited potent antibacterial activities against E. coli, M. tetragenus, and S. aureus with the IZD of 7.00, 14.00, and 12.50 mm, respectively, which were slightly weaker than those of the positive gentamicin sulfate with the IZD of 11.13, 18.30, and 12.13 mm, respectively. In conclusion, our results confirmed that the diversity of gut-associated fungi of C. Servilia could be expected to explore the resource of new species and antibacterial substances.

Pyranone Derivatives With Antitumor Activities, From the Endophytic Fungus Phoma sp. YN02-P-3

Two new pyranone derivatives phomapyrone A (2) and phomapyrone B (3), one new coumarin 11S, 13R-(+)-phomacumarin A (1), three known pyranones (4–6), together with three known amide alkaloids fuscoatramides A-C (7–9), as well as 9S, 11R-(+)-ascosalitoxin (10) were isolated from the endophytic fungus Phoma sp. YN02-P-3, which was isolated from the healthy leaf tissue of a Paulownia tree in Yunnan Province, China. Their structures were elucidated using extensive NMR spectroscopic and HRESIMS data and by comparing the information with literature data. In addition, all compounds were tested for their cytotoxicity activity against human tumor cell lines, and the results showed that new compounds 1-3 showed moderate inhibitory activity against the HL-60 cell line with IC50 values of 31.02, 34.62, and 27.90 μM, respectively.

Suppression of Pepper Root Rot and Wilt Diseases Caused by Rhizoctonia solani and Fusarium oxysporum.

Pepper is vulnerable to soil-borne fungal pathogens such as Rhizoctonia solani and Fusarium oxysporum. The potential of beneficial rhizosphere microorganisms to control R. solani and F. oxysporum f.sp. capsici was evaluated in pepper plants. Paenibacillus polymyxa and Trichoderma longibrachiatum were isolated from rhizospheric soil samples of healthy pepper plants. In vitro, both isolates caused clear reductions in the radial growth of root rot and wilt pathogens. Scanning electron microscopy displayed lysis and abnormal shape of the pathogens in dual cultures with P. polymyxa and T. longibrachiatum. The incidence and severity of root rot and wilt diseases were significantly reduced in pepper plants treated with the growth-promoting fungi (PGPF isolates; Fusarium equiseti GF19-1, Fusarium equiseti GF18-3, and Phoma sp. GS8-3), P. polymyxa, or T. longibrachiatum in comparison to the control. Moreover, the induction treatments led to increased pepper growth compared with their control. The defense related gene (CaPR4) expression was shown to be significantly higher in the treated plants than in the control plants. In conclusion, the antagonistic isolates (P. polymyxa and T. longibrachiatum) and PGPF isolates have a clear impact on the prevention of root rot and wilt diseases in pepper plants incited by R. solani and F. oxysporum f.sp. capsici. The expression of the CaPR4 gene added to the evidence that PGPF isolates generate systemic resistance to pathogen infections.

A New Diphenyl Derivative from Endogenous Phoma sp. Associated with the Edible Mushroom Boletus edulis

A New Diphenyl Derivative from Endogenous Phoma sp. Associated with the Edible Mushroom Boletus edulis

Potential application of Fusarium fungal strains (Fusarium sp. FP, Arthrinium sp. FB, and Phoma sp. FR) for removal of Tl (I) ions from water.

Water pollution caused by heavy metals poses a serious threat to the ecosystem and human health. Among the various treatment techniques for water remediation, adsorption is an efficient method due to its high capacity, low cost, and simplicity. Thallium (Tl) is highly toxic to mammals and its removal from water is gaining increasingly prominent attention. In this study, three fungal strains (Fusarium sp. FP, Arthrinium sp. FB, and Phoma sp. FR) were tested for removal of Tl (I) from aqueous solutions and showed excellent removal performance. The prepared inactive fungal strains were characterized by XRD, FT-IR, SEM, and XPS analyses. The effects of pH, contact time, biomass dosage, and reaction temperature on the removal efficiency of Tl (I) were systematically investigated. The results indicated that the adsorption isotherm data fit well with the Langmuir model, and the pseudo-second-order model was more consistent with the kinetic data description. The maximum adsorption capacity of the fungal strain (Fusarium sp. FP, Arthrinium sp. FB, and Phoma sp. FR) for Tl (I) was found to be 94.69mg/g, 66.97mg/g, and 52.98mg/g, respectively. The thermodynamic data showed that the sorption process was spontaneous and endothermic. The present study showed that the inactive fungal strains could be a promising adsorbent material for Tl (I) removal.

Characterization and biological activities of melanin pigment from root endophytic fungus, Phoma sp. RDSE17.

Melanins are high molecular weight hydrophobic pigments which have gained popularity for their role in virulence against different pathogens. In the present study, we isolated and characterized the melanin pigment produced by a dark septate endophyte fungus Phoma sp. RDSE17, which was associated with the roots of an indigenous Oryza sativa cv. 'Chakhao amubi' in Manipur, Northeast India. The biological properties of purified melanin from the fungus were evaluated for their antioxidant, antimicrobial and anticancerous activities. The pigment was extracted from Phoma sp. by alkaline-acid hydrolysis method and confirmed as melanin through physico-chemical tests and spectral (UV, FTIR, and EPR) analysis. The analyses of the elemental composition indicated that the pigment possessed a low percentage of nitrogen (N) contents, and therefore, would not fall under DOPA class of melanin. Exposure of the fungus to melanin pathway inhibitors revealed a positive melanin inhibition by tricyclazole, but not by kojic acid. Thus, the melanin from Phoma sp. may be a member of the DHN family. Moreover, the purified melanin showed high DPPH (1, 1-Diphenyl-2-picrylhydrazyl) free radical-scavenging activity with an EC50 of 69µg/mL and inhibited human lung cancer cell (A549 cells) proliferation at 80µg/mL. The present study demonstrates that melanin from Phoma sp. RDSE17 could be employed as a potential biological (antioxidant) and antimicrobial agent for inhibiting the growth of humans and phytopathogens.

Evaluation of Phoma sp. Biomass as an Endophytic Fungus for Synthesis of Extracellular Gold Nanoparticles with Antibacterial and Antifungal Properties.

The aim of our study was to examine the different concentrations of AuNPs as a new antimicrobial substance to control the pathogenic activity. The extracellular synthesis of AuNPs performed by using Phoma sp. as an endophytic fungus. Endophytic fungus was isolated from vascular tissue of peach trees (Prunus persica) from Baft, located in Kerman province, Iran. The UltraViolet-Visible Spectroscopy (UV–Vis spectroscopy) and Fourier transform infrared spectroscopy provided the absorbance peak at 526 nm, while the X-ray diffraction and transmission electron microscopy images released the formation of spherical AuNPs with sizes in the range of 10–100 nm. The findings of inhibition zone test of Au nanoparticles (AuNPs) showed a desirable antifungal and antibacterial activity against phytopathogens including Rhizoctonia solani AG1-IA (AG1-IA has been identified as the dominant anastomosis group) and Xanthomonas oryzae pv. oryzae. The highest inhibition level against sclerotia formation was 93% for AuNPs at a concentration of 80 μg/mL. Application of endophytic fungus biomass for synthesis of AuNPs is relatively inexpensive, single step and environmentally friendly. In vitro study of the antifungal activity of AuNPs at concentrations of 10, 20, 40 and 80 μg/mL was conducted against rice fungal pathogen R. solani to reduce sclerotia formation. The experimental data revealed that the Inhibition rate (RH) for sclerotia formation was (15, 33, 74 and 93%), respectively, for their corresponding AuNPs concentrations (10, 20, 40 and 80 μg/mL). Our findings obviously indicated that the RH strongly depend on AuNPs rates, and enhance upon an increase in AuNPs rates. The application of endophytic fungi biomass for green synthesis is our future goal.

Molecular Characterization of Fungi Associated with Smoked Micromesistius poutassou (Blue whiting) from Different Markets in Lagos, Nigeria.

Micromesistius poutassou (Blue whiting) popularly called ‘’Panla’’ in Nigeria. It is one of the affordable fishes imported to Nigeria. With the rising cost of meat, milk and protein foods, consumers have become increasingly interested in fish as a source of protein for its availability and affordability rate. Smoked samples of Micromesistius poutassou were randomly purchased from ten different markets in ten local governments in Lagos state. This collection (purchase) were carried out between June and November 2019 (6 months). The associated fungi were isolated using the pour-plate method and extracted its DNA with the aid of Zymo DNA extraction kit. The extracted fungal DNA were amplified by PCR (Polymerase chain reaction) using specific internal transcribed spacer primer (ITS1/ITS4) and sequenced. Of the total 480 smoked Micromesistius poutassou sampled, ten fungi species were identified and characterised. These fungi include: Kodamaea ohmeri, Daldinia eschscholtzii, Aspergillus longivesica, Aspergillus flavus, Phoma sp, Aspergillus sp, Mucor circinelloides, Aspergillus tamarii, Aspergillus niger, and Geotrichum candidum. Results from this study revealed that smoked Micromesistius poutassou, which are being consumed by Lagosians on the daily basis were heavily contaminated with pathogenic fungi.

A new anti-proliferative compound from an endophytic fungus, Phoma sp.

A new oxazole-type compound (1), named macrooxazole E, and three known macrooxazoles A-C (2–4), were isolated from ethyl acetate (EtOAc) extracts of Phoma sp. JS0228 cultures, an endophytic fungus of Morus alba (M. alba). Structures of the isolated compounds were determined using spectroscopic methods, such as 1 D- and 2 D-nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS). Macrooxazole E (1) differed from macrooxazole C only in the presence of methyl carboxylate instead of free carboxylic acid. Macrooxazole C showed moderate anti-proliferative activities against human breast cancer (MCF-7) and prostate cancer (LNCaP) cell lines with IC50 values of 0.29 mM and 0.36 mM, respectively. This study presents the possibility of the endophytic fungus Phoma sp. JS0228 to produce new bioactive natural compounds.