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Metabolites Mar 2022Plant roots exude a wide variety of secondary metabolites able to attract and/or control a large diversity of microbial species. In return, among the root microbiota,...
Plant roots exude a wide variety of secondary metabolites able to attract and/or control a large diversity of microbial species. In return, among the root microbiota, some bacteria can promote plant development. Among these, are known to produce a wide diversity of secondary metabolites that could have biological activity on the host plant and other soil microorganisms. We previously showed that wheat can interfere with secondary metabolism production through its root metabolites. Interestingly, production of bioactive metabolites, such as phloroglucinol, phenazines, pyrrolnitrin, or acyl homoserine lactones, are modified in the presence of wheat root extracts. A new cross metabolomic approach was then performed to evaluate if wheat metabolic interferences on secondary metabolites production have consequences on wheat metabolome itself. Two different strains were conditioned by wheat root extracts from two genotypes, leading to modification of bacterial secondary metabolites production. Bacterial cells were then inoculated on each wheat genotypes. Then, wheat root metabolomes were analyzed by untargeted metabolomic, and metabolites from the Adular genotype were characterized by molecular network. This allows us to evaluate if wheat differently recognizes the bacterial cells that have already been into contact with plants and highlights bioactive metabolites involved in wheat- interaction.
PubMed: 35323679
DOI: 10.3390/metabo12030236 -
PloS One 2022Fludioxonil and iprodione are effective fungicides widely used for crop protection and are essential for controlling plant pathogenic fungi. The emergence of...
Fludioxonil and iprodione are effective fungicides widely used for crop protection and are essential for controlling plant pathogenic fungi. The emergence of fungicide-resistant strains of targeted pathogens is regularly monitored, and several cases have been reported. Non-targeted fungi may also be exposed to the fungicide residues in agricultural fields. However, there are no comprehensive reports on fungicide-resistant strains of non-targeted fungi. Here, we surveyed 99 strains, representing 12 Penicillium species, that were isolated from a variety of environments, including foods, dead bodies, and clinical samples. Among the Penicillium strains, including non-pathogenic P. chrysogenum and P. camembertii, as well as postharvest pathogens P. expansum and P. digitatum, 14 and 20 showed resistance to fludioxonil and iprodione, respectively, and 6 showed multi-drug resistance to the fungicides. Sequence analyses revealed that some strains of P. chrysogenum and Penicillium oxalicum had mutations in NikA, a group III histidine kinase of the high-osmolarity glycerol pathway, which is the mode of action for fludioxonil and iprodione. The single nucleotide polymorphisms of G693D and T1318P in P. chrysogenum and T960S in P. oxalicum were only present in the fludioxonil- or iprodione-resistant strains. These strains also exhibited resistance to pyrrolnitrin, which is the lead compound in fludioxonil and is naturally produced by some Pseudomonas species. This study demonstrated that non-targeted Penicillium strains distributed throughout the environment possess fungicide resistance.
Topics: Aminoimidazole Carboxamide; Cadaver; Crops, Agricultural; Dioxoles; Drug Resistance, Fungal; Food Analysis; Fungal Proteins; Fungicides, Industrial; Humans; Hydantoins; Mycoses; Penicillium; Polymorphism, Single Nucleotide; Pyrroles
PubMed: 35100282
DOI: 10.1371/journal.pone.0262521 -
Microorganisms Oct 2021The application and promotion of biological control agents are limited because of poor efficacy and unstable performance in the field. Screening microorganisms with high...
The application and promotion of biological control agents are limited because of poor efficacy and unstable performance in the field. Screening microorganisms with high antagonistic activity, effective adaptability, and high field-survival should be prospected. Myxobacteria are soil predatory bacteria with wide adaptability, which are considered as good antagonists. Here, we report a myxobacterium strain M34 isolated from subtropical forest soil in South China using the baiting method. Based on the morphological observation, physiological test, biochemical characteristics, 16S rRNA gene sequence, and genomic data, strain M34 was identified as a novel genus and novel species, representing a new clade of Myxococcaceae, for which the name gen. nov. sp. nov. is proposed (type strain M34 = GDMCC 1.2275 = KCTC 82453). The typical features of M34, including fruiting body formation and extracellular fibrillar interconnection, indicated by microscopic observations, contributed to cell adaption in different environments. Furthermore, the strain showed antifungal activity against phytopathogenic fungi and predatory activity to both Gram-negative and Gram-positive phytopathogenic bacteria. The bioprotective mechanisms are attributed to the presence of pyrrolnitrin and derivative with antifungal activity and the extracellular proteins with lytic activity against pathogenic bacteria. Due to its multiple beneficial traits, strain M34 has the potential to be developed into a versatile biocontrol agent for the management of both fungal and bacterial phytopathogens.
PubMed: 34683458
DOI: 10.3390/microorganisms9102137 -
Microorganisms Sep 2021The bacterial pathogen causes the destructive fruit blotch (BFB) on cucurbit plants. YL-1 is a bacterial strain isolated from Mississippi soil and its genome harbors...
The bacterial pathogen causes the destructive fruit blotch (BFB) on cucurbit plants. YL-1 is a bacterial strain isolated from Mississippi soil and its genome harbors some antimicrobial-related gene clusters, such as phenazine, pyrrolnitrin, and pyoverdine. Here, we evaluated the antimicrobial activity of strain YL-1 as compared with its deficient mutants of antimicrobial-related genes, which were obtained using a based site-specific mutagenesis strategy. We found that only phenazine-deficient mutants Δ and Δ almost lost the inhibitory effects against in LB plates compared with the wild-type strain YL-1, and that the main antibacterial compound produced by strain YL-1 in LB medium was phenazine-1-carboxylic acid (PCA) based on the liquid chromatography-mass spectrometry (LC-MS) analysis. Gene expression analyses revealed that PCA enhanced the accumulation of reactive oxygen species (ROS) and increased the activity of catalase (CAT) in . The inhibition effect of PCA against was lowered by adding exogenous CAT. PCA significantly upregulated the transcript level of from 6 to 10 h, which encodes CAT that helps to protect the bacteria against oxidative stress. Collectively, the findings of this research suggest PCA is one of the key antimicrobial metabolites of bacterial strain YL-1, a promising biocontrol agent for disease management of BFB of cucurbit plants.
PubMed: 34683333
DOI: 10.3390/microorganisms9102012 -
Frontiers in Fungal Biology 2021is a major fungal pathogen causing life threatening infections in immunocompromised humans and certain animals. The HOG pathway is for two reasons interesting in this...
is a major fungal pathogen causing life threatening infections in immunocompromised humans and certain animals. The HOG pathway is for two reasons interesting in this context: firstly, it is a stress signaling pathway that contributes to the ability of this pathogen to adapt to various stress conditions and secondly, it is the target of antifungal agents, such as fludioxonil or pyrrolnitrin. In this study, we demonstrate that Ypd1 is an essential protein in . As the central component of the multistep phosphorelay it represents the functional link between the sensor histidine kinases and the downstream response regulators SskA and Skn7. A GFP-Ypd1 fusion was found to reside in both, the cytoplasm and the nucleus and this pattern was only slightly affected by fludioxonil. A strain in which the 1 gene is expressed from a tet-on promoter construct is unable to grow under non-inducing conditions and shows the characteristic features of wild type hyphae treated with fludioxonil. Expression of wild type Ypd1 prevents this lethal phenotype, but expression of an Ypd1 mutant protein lacking the conserved histidine at position 89 was unable to do so, which confirms that Ypd1 is a phosphotransfer protein. Generation of 1 variants of several mutant strains revealed that the lethal phenotype associated with low amounts of Ypd1 depends on SskA, but not on TcsC or Skn7. The ΔA 1, but not the ΔAΔ7 1 mutant, was sensitive to fludioxonil, which underlines the importance of Skn7 in this context. We finally succeeded to delete 1, but only if A and 7 were both inactivated, not in a ΔA single mutant. Hence, a deletion of 1 and an inactivation of Ypd1 by fludioxonil result in similar phenotypes and the two response regulators SskA and Skn7 are involved in both processes albeit with a different relative importance.
PubMed: 37744118
DOI: 10.3389/ffunb.2021.756990 -
PloS One 2021The endophytic bacterium Burkholderia contaminans NZ was isolated from jute, which is an important fiber-producing plant. This bacterium exhibits significant growth...
The endophytic bacterium Burkholderia contaminans NZ was isolated from jute, which is an important fiber-producing plant. This bacterium exhibits significant growth promotion activity in in vivo pot experiments, and like other plant growth-promoting (PGP) bacteria fixes nitrogen, produces indole acetic acid (IAA), siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. B. contaminans NZ is considered to exert a promising growth inhibitory effect on Macrophomina phaseolina, a phytopathogen responsible for infecting hundreds of crops worldwide. This study aimed to identify the possibility of B. contaminans NZ as a safe biocontrol agent and assess its effectiveness in suppressing phytopathogenic fungi, especially M. phaseolina. Co-culture of M. phaseolina with B. contaminans NZ on both solid and liquid media revealed appreciable growth suppression of M. phaseolina and its chromogenic aberration in liquid culture. Genome mining of B. contaminans NZ using NaPDoS and antiSMASH revealed gene clusters that displayed 100% similarity for cytotoxic and antifungal substances, such as pyrrolnitrin. GC-MS analysis of B. contaminans NZ culture extracts revealed various bioactive compounds, including catechol; 9,10-dihydro-12'-hydroxy-2'-methyl-5'-(phenylmethyl)- ergotaman 3',6',18-trione; 2,3-dihydro-3,5- dihydroxy-6-methyl-4H-pyran-4-one; 1-(1,6-Dioxooctadecyl)- pyrrolidine; 9-Octadecenamide; and 2- methoxy- phenol. These compounds reportedly exhibit tyrosinase inhibitory, antifungal, and antibiotic activities. Using a more targeted approach, an RP-HPLC purified fraction was analyzed by LC-MS, confirming the existence of pyrrolnitrin in the B. contaminans NZ extract. Secondary metabolites, such as catechol and ergotaman, have been predicted to inhibit melanin synthesis in M. phaseolina. Thus, B. contaminans NZ appears to inhibit phytopathogens by apparently impairing melanin synthesis and other potential biochemical pathways, exhibiting considerable fungistatic activity.
Topics: Ascomycota; Biological Control Agents; Burkholderia; Coculture Techniques; Crops, Agricultural; Endophytes; Gas Chromatography-Mass Spectrometry; Indoleacetic Acids; Melanins; Nitrogen Fixation; Pyrrolnitrin; Whole Genome Sequencing
PubMed: 34591915
DOI: 10.1371/journal.pone.0257863 -
Microbes and Environments 2021Biocontrol fluorescent pseudomonads produce a number of antibiotic organic compounds, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, and phenazine. We...
Biocontrol fluorescent pseudomonads produce a number of antibiotic organic compounds, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, and phenazine. We previously classified rhizospheric fluorescent pseudomonads harboring antibiotic biosynthetic gene clusters into 10 operational taxonomic units (OTUs). In the present study, we report the complete genome sequences of selected strains from these OTUs. The genetic diversity of antibiotic biosynthetic gene clusters and their surrounding sequences correlated with the OTU classification. In comparisons of the biocontrol activity and distribution of antibiotic biosynthetic gene clusters, we found that the pyrrolnitrin biosynthetic gene cluster more effectively controlled the growth of Rhizoctonia solani.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Genome, Bacterial; Multigene Family; Pseudomonas fluorescens; Rhizoctonia; Soil Microbiology
PubMed: 34321367
DOI: 10.1264/jsme2.ME21034 -
Molecular Plant Pathology Aug 2021The biocontrol rhizobacterium Pseudomonas protegens H78 can produce a large array of antimicrobial secondary metabolites, including pyoluteorin (Plt),...
The biocontrol rhizobacterium Pseudomonas protegens H78 can produce a large array of antimicrobial secondary metabolites, including pyoluteorin (Plt), 2,4-diacetylphloroglucinol (DAPG), and pyrrolnitrin (Prn). Our preliminary study showed that the biosynthesis of antibiotics including Plt is activated by the RNA chaperone Hfq in P. protegens H78. This prompted us to explore the global regulatory mechanism of Hfq, as well as the catabolite repression control (Crc) protein in H78. The antimicrobial capacity of H78 was positively controlled by Hfq while slightly down-regulated by knockout of crc. Similarly, cell growth of H78 was significantly impaired by deletion of hfq and slightly inhibited by knockout of crc. Transcriptomic profiling revealed that hfq mutation resulted in significant down-regulation of 688 genes and up-regulation of 683 genes. However, only 113 genes were significantly down-regulated and 105 genes up-regulated by the crc mutation in H78. Hfq positively regulated the expression of gene clusters involved in secondary metabolism (plt, prn, phl, hcn, and pvd), the type VI secretion system, and aromatic compound degradation. However, Crc only positively regulated the biosynthesis of Plt but not other antibiotics. Hfq also regulated expression of genes involved in oxidative phosphorylation and flagellar biogenesis. In addition, Hfq and Crc activated transcription of crcY/Z sRNAs by feedback. In summary, Hfq processes far more extensive and intensive regulatory capacity than Crc and shows small cross-regulation with Crc in H78. This study lays the foundation for clarifying the Hfq and/or Crc-dependent global regulatory network and improving antibiotic production by genetic engineering in P. protegens.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Gene Expression Regulation, Bacterial; Pseudomonas
PubMed: 33963656
DOI: 10.1111/mpp.13070 -
Applied and Environmental Microbiology Jun 2021Within animal-associated microbiomes, the functional roles of specific microbial taxa are often uncharacterized. Here, we use the fungus-growing ant system, a model for...
Within animal-associated microbiomes, the functional roles of specific microbial taxa are often uncharacterized. Here, we use the fungus-growing ant system, a model for microbial symbiosis, to determine the potential defensive roles of key bacterial taxa present in the ants' fungus gardens. Fungus gardens serve as an external digestive system for the ants, with mutualistic fungi in the genus converting the plant substrate into energy for the ants. The fungus garden is host to specialized parasitic fungi in the genus . Here, we examine the potential role of spp. that occur within ant fungus gardens in inhibiting We isolated members of the bacterial genera and from 50% of the 52 colonies sampled, indicating that members of the family are common inhabitants in the fungus gardens of a diverse range of fungus-growing ant genera. Using antimicrobial inhibition bioassays, we found that 28 out of 32 isolates inhibited at least one strain with a zone of inhibition greater than 1 cm. Genomic assessment of fungus garden-associated indicated that isolates with strong inhibition all belonged to the genus and contained biosynthetic gene clusters that encoded the production of two antifungals: burkholdine1213 and pyrrolnitrin. Organic extracts of cultured isolates confirmed that these compounds are responsible for antifungal activities that inhibit but, at equivalent concentrations, not spp. Overall, these new findings, combined with previous evidence, suggest that members of the fungus garden microbiome play an important role in maintaining the health and function of fungus-growing ant colonies. Many organisms partner with microbes to defend themselves against parasites and pathogens. Fungus-growing ants must protect spp., the fungal mutualist that provides sustenance for the ants, from a specialized fungal parasite, . The ants take multiple approaches, including weeding their fungus gardens to remove spores, as well as harboring spp., bacteria that produce antifungals that inhibit In addition, a genus of bacteria commonly found in fungus gardens, , is known to produce secondary metabolites that inhibit spp. In this study, we isolated spp. from fungus-growing ants, assessed the isolates' ability to inhibit spp., and identified two compounds responsible for inhibition. Our findings suggest that spp. are often found in fungus gardens, adding another possible mechanism within the fungus-growing ant system to suppress the growth of the specialized parasite .
Topics: Animals; Antifungal Agents; Ants; Burkholderia; Hypocreales; Lipopeptides; Microbiota; Multigene Family; Parasites; Phylogeny; Pyrrolnitrin; Symbiosis
PubMed: 33962985
DOI: 10.1128/AEM.00178-21 -
Scientific Reports Mar 2021Aspergillus fumigatus is an important fungal pathogen that represents a major threat for severely immunocompromised patients. Cases of invasive aspergillosis are...
Aspergillus fumigatus is an important fungal pathogen that represents a major threat for severely immunocompromised patients. Cases of invasive aspergillosis are associated with a high mortality rate, which reflects the limited treatment options that are currently available. The development of novel therapeutic approaches is therefore an urgent task. An interesting compound is fludioxonil, a derivative of the bacterial secondary metabolite pyrrolnitrin. Both agents possess potent antimicrobial activity against A. fumigatus and trigger a lethal activation of the group III hybrid histidine kinase TcsC, the major sensor kinase of the High Osmolarity Glycerol (HOG) pathway in A. fumigatus. In the current study, we have characterized proteins that operate downstream of TcsC and analyzed their roles in the antifungal activity of fludioxonil and in other stress situations. We found that the SskA-SakA axis of the HOG pathway and Skn7 can independently induce an increase of the internal glycerol concentration, but each of these individual responses amounts for only half of the level found in the wild type. The lethal fludioxonil-induced ballooning occurs in the sskA and the sakA mutant, but not in the skn7-deficient strain, although all three strains show comparable glycerol responses. This indicates that an elevated osmotic pressure is necessary, but not sufficient and that a second, decisive and Skn7-dependent mechanism mediates the antifungal activity. We assume that fludioxonil triggers a reorganization in the fungal cell wall that reduces its rigidity, which in combination with the elevated osmotic pressure executes the lethal expansion of the fungal cells. Two findings link Skn7 to the cell wall of A. fumigatus: (1) the fludioxonil-induced massive increase in the chitin content depends on Skn7 and (2) the skn7 mutant is more resistant to the cell wall stressor Calcofluor white. In conclusion, our data suggest that the antifungal activity of fludioxonil in A. fumigatus relies on two distinct and synergistic processes: A high internal osmotic pressure and a weakened cell wall. The involvement of Skn7 in both processes most likely accounts for its particular importance in the antifungal activity of fludioxonil.
Topics: Antifungal Agents; Aspergillus fumigatus; Dioxoles; Fungal Proteins; Pyrroles
PubMed: 33674651
DOI: 10.1038/s41598-021-84740-6