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Microorganisms Apr 2024In the continuous cropping of , the pathogenic fungi in the rhizosphere soil increased and infected the roots of , resulting in a decrease in yield. This is an urgent...
In the continuous cropping of , the pathogenic fungi in the rhizosphere soil increased and infected the roots of , resulting in a decrease in yield. This is an urgent problem that needs to be solved in order to effectively overcome the obstacles associated with the continuous cropping of . Previous studies have shown that inhibits pathogenic fungi in the rhizosphere of , but the inhibitory effect was not stable. Therefore, we hope to introduce biochar to help colonize in soil. In the experiment, fields planted with for 5 years were renovated, and biochar was mixed in at the same time. The applied amount of biochar was set to four levels (B0, 10 kg·hm; B1, 80 kg·hm; B2, 110 kg·hm; B3, 140 kg·hm), and biological agent was set to three levels (C1, 10 kg·hm; C2, 15 kg·hm; C3, 25 kg·hm). The full combination experiment and a blank control group (CK) were used. The experimental results show that the overall decreased by 0.86%~65.68% at the phylum level. increased by -73.81%~138.47%, and increased by -51.27%~403.20%. At the genus level, increased by -10.29%~855.44%, decreased by 35.02%~86.79%, and increased by -93.60%~680.62%. mainly causes acute bacterial wilt root rot, while mainly causes yellow rot. Under different treatments, the Shannon index increased by -6.77%~62.18%, the Chao1 index increased by -12.07%~95.77%, the Simpson index increased by -7.31%~14.98%, and the ACE index increased by -11.75%~96.12%. The good_coverage indices were all above 0.99. The results of a random forest analysis indicated that , , and were the top three most important species in the soil, with MeanDecreaseGini values of 2.70, 2.50, and 2.45, respectively. , the primary pathogen of , ranked fifth, and its MeanDecreaseGini value was 2.28. The experimental results showed that the B2C2 treatment had the best inhibitory effect on , and the relative abundance of in rhizosphere soil decreased by 86.79% under B2C2 treatment; the B1C2 treatment had the best inhibitory effect on , and the relative abundance of in the rhizosphere soil decreased by 93.60% under B1C2 treatment. Therefore, if we want to improve the soil with acute Ralstonia solanacearum root rot, we should use the B2C2 treatment to improve the soil environment; if we want to improve the soil with yellow rot disease, we should use the B1C2 treatment to improve the soil environment.
PubMed: 38674727
DOI: 10.3390/microorganisms12040783 -
Marine Drugs Jan 2024Co-cultivation, coupled with the OSMAC approach, is considered an efficient method for expanding microbial chemical diversity through the activation of cryptic...
Co-cultivation, coupled with the OSMAC approach, is considered an efficient method for expanding microbial chemical diversity through the activation of cryptic biosynthetic gene clusters (BGCs). As part of our project aiming to discover new fungal metabolites for crop protection, we previously reported five polyketides, the macrolides dendrodolides E () and N (), the azaphilones spiciferinone () and 8-hydroxy-spiciferinone (), and the -naphtho--pyrone cephalochromin () from the solid Potato Dextrose Agar (PDA) co-culture of two marine sediment-derived fungi, and . However, some of the purified metabolites could not be tested due to their minute quantities. Here we cultivated these fungi (both axenic and co-cultures) in liquid regime using three different media, Potato Dextrose Broth (PDB), Sabouraud Dextrose Broth (SDB), and Czapek-Dox Broth (CDB), with or without shaking. The aim was to determine the most ideal co-cultivation conditions to enhance the titers of the previously isolated compounds and to produce extracts with stronger anti-phytopathogenic activity as a basis for future upscaled fermentation. Comparative metabolomics by UPLC-MS/MS-based molecular networking and manual dereplication was employed for chemical profiling and compound annotations. Liquid co-cultivation in PDB under shaking led to the strongest activity against the phytopathogen . Except for compound , all target compounds were detected in the co-culture in PDB. Compounds and were produced in lower titers, whereas the azaphilones ( and ) were overexpressed in PDB compared to PDA. Notably, liquid PDB co-cultures contained meroterpenoids and depside clusters that were absent in the solid PDA co-cultures. This study demonstrates the importance of culture regime in BGC regulation and chemical diversity of fungal strains in co-culture studies.
Topics: Coculture Techniques; Chromatography, Liquid; Tandem Mass Spectrometry; Metabolome; Culture Media; Glucose
PubMed: 38393037
DOI: 10.3390/md22020066 -
International Journal of Molecular... Aug 2023Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the tree stands of protected areas, which...
Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the tree stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plants. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing. Saprotrophs dominated in the studied rhizospheres, but their percentage share decreased with the age of the development group (for 51.91 from 43.13%). However, in the case of mycorrhizal fungi, an opposite trend was observed (16.96-26.75%). The most numerous genera were: saprotrophic (2.54-3.83%), (6.47-12.86%), (1.39-11.78%), pathogenic (0.53-4.39%), and mycorrhizal (1.80-5.46%), (2.94-5.64%) and (4.54-15.94%). The species composition of rhizosphere fungal communities was favorable for the regeneration of natural spruce and the development of multi-generational Norway spruce stands. The ratio of the abundance of saprotrophic and mycorrhizal fungi to the abundance of pathogens was high and promising for the durability of the large proportion of spruce in the Wigry National Park and for forest ecosystems in general.
Topics: Rhizosphere; Abies; Picea; Poland; Parks, Recreational; Mycorrhizae; Pinus; Microbiota; Norway
PubMed: 37628809
DOI: 10.3390/ijms241612628 -
Medical Mycology Case Reports Sep 2023A mycotic infection manifesting as abdominal distension with free serous fluid accumulation in the coelomic cavity is documented in farmed rainbow trout. Histological...
A mycotic infection manifesting as abdominal distension with free serous fluid accumulation in the coelomic cavity is documented in farmed rainbow trout. Histological examination using PAS and silver staining revealed the presence of numerous fungal hyphae in the spleen and gastrointestinal wall. The isolated fungus was sterile and identified by using phylogenetic analysis based on four loci as . This is the first time this fungus has been reported as pathogen.
PubMed: 37274730
DOI: 10.1016/j.mmcr.2023.05.001 -
Molecular Biology Reports May 2023Shot hole is one of the important fungal diseases in stone fruits viz., peach, plum, apricot and cherry caused by Wilsonomyces carpophilus and almond among nut crops....
Whole genome sequencing of Wilsonomyces carpophilus, an incitant of shot hole disease in stone fruits: insights into secreted proteins of a necrotrophic fungal repository.
BACKGROUND
Shot hole is one of the important fungal diseases in stone fruits viz., peach, plum, apricot and cherry caused by Wilsonomyces carpophilus and almond among nut crops. Fungicides significantly decrease the disease. Pathogenicity studies proved a wide host range of the pathogen infecting all stone fruits and almond among the nut crops, however, the mechanism underlying host-pathogen interaction is still unknown. Molecular detection of the pathogen using polymerase chain reaction (PCR) based simple sequence repeat (SSR) markers is also unknown due to the unavailability of the pathogen genome.
METHODS AND RESULTS
We examined the morphology, pathology and genomics of the Wilsonomyces carpophilus. Whole genome sequencing of the W. carpophilus was carried out by Illumina HiSeq and PacBio high throughput sequencing plate-forms through hybrid assembly. Constant selection pressure alters the molecular mechanism of the pathogen causing disease. The studies revealed that the necrotrophs are more lethal with a complex pathogenicity mechanism and little-understood effector repositories. The different isolates of necrotrophic fungus W. carpophilus causing shot hole in stone fruits namely peach, plum, apricot and cherry, and almonds among the nut crops showed a significant variation in their morphology, however, the probability value (p = 0.29) suggests in-significant difference in the pathogenicity. Here, we reported draft genome of W. carpophilus of size 29.9 Mb (Accession number: PRJNA791904). A total of 10,901 protein-coding genes were predicted, including heterokaryon incompatibility genes, cytochrome-p450 genes, kinases, sugar transporters among others. We found 2851 simple sequence repeats (SSRs), tRNAs, rRNAs and pseudogenes in the genome. The most prominent proteins showing necrotrophic lifestyle of the pathogen were hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic, and proteolytic enzymes accounted for 225 released proteins. Among the 223 fungal species, top-hit species distribution revealed the majority of hits against the Pyrenochaeta species followed by Ascochyta rabiei and Alternaria alternata.
CONCLUSION
Draft genome of W. carpophilus is 29.9 Mb based on Illumina HiSeq and PacBio hybrid assembly. The necrotrophs are more lethal with a complex pathogenicity mechanism. A significant variation in morphology was observed in different pathogen isolates. A total of 10,901 protein-coding genes were predicted in the pathogen genome including heterokaryon incompatibility, cytochrome-p450 genes, kinases and sugar transporters. We found 2851 SSRs, tRNAs, rRNAs and pseudogenes, and prominent proteins showing necrotrophic lifestyle such as hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic and proteolytic enzymes. The top-hit species distribution were against the Pyrenochaeta spp. followed by Ascochyta rabiei.
Topics: Fruit; Prunus domestica; Whole Genome Sequencing; Peptide Hydrolases; Cytochromes; Sugars
PubMed: 36877348
DOI: 10.1007/s11033-023-08243-5 -
Plant Disease Sep 2023Corky root rot is an important disease in tomato production systems and is caused by and (formerly Types 1 and 2, respectively). The corky root rot pathogens are slow...
Corky root rot is an important disease in tomato production systems and is caused by and (formerly Types 1 and 2, respectively). The corky root rot pathogens are slow growing and difficult to isolate and quantify in soil and plant tissue. A multiplex hydrolysis probe-based qPCR assay was designed to allow for simultaneous detection and quantification of and with a competitive internal control to indicate if qPCR inhibitors are present. Single species and multiplex assays for spp. detected DNA levels above 0.013 pg of DNA per reaction. These highly specific assays had no nontarget amplification of other fungal and oomycete pathogens or rhizosphere-associated fungi of tomatoes that were tested. This assay can be used to quantify populations in roots and soils in tomato production systems to better determine the impacts of disease management strategies on spp. and provides a tool to study the biology of spp.
Topics: Solanum lycopersicum; Plant Diseases; Polymerase Chain Reaction; DNA
PubMed: 36774576
DOI: 10.1094/PDIS-08-22-2009-RE -
Journal of Fungi (Basel, Switzerland) Dec 2022Coelomycetous fungi are among the emerging causes of infections and have been involved in many kinds of infections, including keratitis and endophtalmitis. Here, we...
Coelomycetous fungi are among the emerging causes of infections and have been involved in many kinds of infections, including keratitis and endophtalmitis. Here, we present the first case of keratitis caused by a coelomycetous fungus belonging to the family Cucurbitariaceae. In this case report, we describe the clinical presentation of a 56-year-old woman, a regular contact lens wearer, who was treated for pain in her right eye and fixed spot vision after an injury with plant debris. On examination, a corneal ulcer was observed, the foreign body was removed, and topical eye-drop therapy was started. After an initial improvement, the patient returned three weeks later due to a recurrence of discomfort in her right eye, observing the persistence of the corneal ulcer. Corneal scrapings were taken for culture, growing a filamentous fungus after seven days, which was identified by sequencing the fungal internal transcribed spacer region. It should be noted that microbiological identification of the coelomycetes in the clinical laboratory is not easy because of their difficulty in sporulating, making molecular techniques based on the amplification and sequencing of appropriate phylogenetic markers essential. Identification of these fungi is mandatory in order to optimise treatment due to the difficulty in eradicating them with antifungal treatment, requiring surgery in 50% of cases.
PubMed: 36675829
DOI: 10.3390/jof9010008 -
American Journal of Ophthalmology Case... Dec 2022(syn. ) is a rare fungal species belonging to the Coelomycetes group, mostly isolated from infected nails and skin.We present a case of contact lens-related fungal...
PURPOSE
(syn. ) is a rare fungal species belonging to the Coelomycetes group, mostly isolated from infected nails and skin.We present a case of contact lens-related fungal keratitis caused by .
OBSERVATIONS
We present a case of a 69-year-old woman with multiple risk factors for a fungal keratitis including ophthalmological history of herpetic keratitis, contact lens wear and chronic steroid use. At presentation, the corneal ulcer resembled a recurrent herpetic keratitis but evolved into a more dense stromal infiltrate despite antiviral therapy. Microscopic examination, culture and staining of corneal tissue obtained by scraping showed mycelia. PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry confirmed the presence of . Topical antifungal treatment was able to dim the inflammation. Because of a persistent epithelial defect, an amniotic membrane transplantation was performed. Although corneal epithelium was restored, stromal scarring in the visual axis resulted in substantial vision loss.
CONCLUSIONS
To our knowledge no other cases of fungal keratitis caused by have been described Early diagnosis can allow prompt initiation of antifungal treatment, which should be guided by susceptibility testing.
PubMed: 36312788
DOI: 10.1016/j.ajoc.2022.101731 -
Applied Microbiology and Biotechnology Sep 2022Smokeless tobacco (SLT) alters the oral microbiome of smokeless tobacco users. Dysbiosis of oral bacteriome has been determined; however, the mycobiome of SLT users has...
Smokeless tobacco (SLT) alters the oral microbiome of smokeless tobacco users. Dysbiosis of oral bacteriome has been determined; however, the mycobiome of SLT users has not been characterized. The oral mycobiome was assayed by amplification and sequencing of the fungal internal transcribed spacer (ITS1) region from oral swab samples of non-SLT users, SLT users (with or without oral lesions), and SLT with alcohol users. We observed that the richness and diversity of oral mycobiome were significantly decreased in SLT with oral lesions users than in non-users. The β-diversity analysis showed significant dissimilarity of oral mycobiome between non-users and SLT with oral lesions users. Linear discriminant analysis effect size and random forest analysis of oral mycobiome affirm that the genus Pichia was typical for SLT with oral lesions users. Prevalence of the fungal genus Pichia correlates positively with Starmerella, Mortierella, Fusarium, Calonectria, and Madurella, but is negatively correlated with Pyrenochaeta, Botryosporium, and Alternaria. Further, the determination of oral mycobiome functionality showed a high abundance of pathotroph-saprotroph-symbiotroph and animal pathogen-endophyte-epiphyte-undefined saprotroph at trophic and guild levels, respectively, indicating possibly major changes in normal growth repression of types of fungi. The oral mycobiome in SLT users was identified and comprehensively analyzed for the first time. SLT intake is associated with oral mycobiome dysbiosis and such alterations of the oral mycobiome may contribute to oral carcinogenesis in SLT users. This study will provide a basis for further large-scale investigations on the potential role of the mycobiome in SLT-induced oral cancer. KEY POINTS: • SLT induces dysbiosis of the oral microbiome that can contribute to oral cancer. • Oral mycobiome diversity is noticeably reduced in SLT users having oral lesions. • Occurrence of Pichia can be used as a biomarker for SLT users having oral lesions.
Topics: Dysbiosis; Humans; Mouth Neoplasms; Mycobiome; Pilot Projects; Tobacco Use; Tobacco, Smokeless
PubMed: 35913514
DOI: 10.1007/s00253-022-12096-6 -
Marine Drugs Jun 2022Mangrove-associated fungi are rich sources of novel and bioactive compounds. A total of 102 fungal strains were isolated from the medicinal mangrove collected from the...
Mangrove-associated fungi are rich sources of novel and bioactive compounds. A total of 102 fungal strains were isolated from the medicinal mangrove collected from the South China Sea. Eighty-four independent culturable isolates were identified using a combination of morphological characteristics and internal transcribed spacer (ITS) sequence analyses, of which thirty-seven strains were selected for phylogenetic analysis. The identified fungi belonged to 22 genera within seven taxonomic orders of one phyla, of which four genera , , , and were first isolated from mangroves. The cytotoxic activity of organic extracts from 55 identified fungi was evaluated against human lung cancer cell lines (A-549), human cervical carcinoma cell lines (HeLa), human hepatoma cells (HepG2), and human acute lymphoblastic leukemia cell lines (Jurkat). The crude extracts of 31 fungi (56.4%) displayed strong cytotoxicity at the concentration of 50 μg/mL. Furthermore, the fungus sp. (HS-N-27) still showed strong cytotoxic activity at the concentration of 25 µg/mL. Integrating cytotoxic activity-guided strategy and fingerprint analysis, a well-known natural Golgi-disruptor and Arf-GEFs inhibitor, brefeldin A, was isolated from the target active strain HS-N-27. It displayed potential activity against A549, HeLa and HepG2 cell lines with the IC values of 101.2, 171.9 and 239.1 nM, respectively. Therefore, combining activity-guided strategy with fingerprint analysis as a discovery tool will be implemented as a systematic strategy for quick discovery of active compounds.
Topics: Acanthaceae; Antineoplastic Agents; Ascomycota; Brefeldin A; Fungi; Gene Library; Humans; Phylogeny
PubMed: 35877725
DOI: 10.3390/md20070432