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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Golic D, Gobbi A, Maiorano A, Pautasso M, Reignault PL. Pest categorisation of Pyrrhoderma noxium. EFSA J 2024; 22:e8667. [PMID: 38505477 PMCID: PMC10949325 DOI: 10.2903/j.efsa.2024.8667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Following the commodity risk assessment of bonsai plants (Pinus parviflora grafted on Pinus thunbergii) from China performed by EFSA, the EFSA Plant Health Panel performed a pest categorisation of Pyrrhoderma noxium, a clearly defined plant pathogenic basidiomycete fungus of the order Hymenochaetales and the family Hymenochaetaceae. The pathogen is considered as opportunistic and has been reported on a wide range of hosts, mainly broad-leaved and coniferous woody plants, causing root rots. In addition, the fungus was reported to live saprophytically on woody substrates and was isolated as an endophyte from a few plant species. This pest categorisation focuses on the hosts that are relevant for the EU (e.g. Citrus, Ficus, Pinus, Prunus, Pyrus, Quercus and Vitis vinifera). Pyrrhoderma noxium is present in Africa, Central and South America, Asia and Oceania. It has not been reported in the EU. Pyrrhoderma noxium is not included in Commission Implementing Regulation (EU) 2019/2072. Plants for planting (excluding seeds), bark and wood of host plants as well as soil and other growing media associated with plant debris are the main pathways for the entry of the pathogen into the EU. Host availability and climate suitability factors occurring in parts of the EU are favourable for the establishment and spread of the pathogen. The introduction and spread of the pathogen into the EU are expected to have an economic and environmental impact in parts of the territory where hosts are present. Phytosanitary measures are available to prevent the introduction and spread of the pathogen into the EU. Pyrrhoderma noxium satisfies all the criteria that are within the remit of EFSA to assess for this species to be regarded as potential Union quarantine pest.
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Adra C, Tran TD, Foster K, Tomlin R, Kurtböke Dİ. Identification of Acetomycin as an Antifungal Agent Produced by Termite Gut-Associated Streptomycetes against Pyrrhoderma noxium. Antibiotics (Basel) 2024; 13:45. [PMID: 38247604 PMCID: PMC10812552 DOI: 10.3390/antibiotics13010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
Plant fungal pathogen Pyrrhoderma noxium is responsible for the destructive and invasive disease of brown root rot currently affecting the city of Brisbane, Australia. In order to address this issue, environmentally friendly and safe alternatives to chemical control are preferred due to the city's public setting. Antifungal natural products are ideal candidates as biological control alternatives and can be detected through investigating the metabolomes of microbial symbionts. Within this study, an NMR-based metabolomics approach was applied to fermentation extracts obtained from 15 termite gut-associated streptomycetes. By analysing the NMR spectra, six of the extracts which displayed similar chemical profiles exhibited antifungal activity against the P. noxium pathogen. The major compound within these extracts was identified as acetomycin using NMR and X-ray crystallography analyses. This is the first reporting of acetomycin as a potential natural product fungicide, particularly as an antifungal agent against P. noxium. Inhibitory activity was also found against other important fungal crop pathogens, including Aspergillus niger, Botrytis cinerea, and Alteranaria alternata. Further experimentation using a woodblock test found inhibitory activity on the growth of the P. noxium pathogen for up to 3 weeks and a significant difference in the integrity of the woodblocks when conducting compression strength tests after 6 weeks. Therefore, acetomycin may be used as a biological control agent and natural product fungicide against P. noxium.
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Affiliation(s)
- Cherrihan Adra
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia; (C.A.); (T.D.T.)
| | - Trong D. Tran
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia; (C.A.); (T.D.T.)
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia
| | - Keith Foster
- Brisbane City Council, Program, Planning and Integration, Brisbane Square, Level 10, 266 George Street, Brisbane, QLD 4000, Australia; (K.F.); (R.T.)
| | - Russell Tomlin
- Brisbane City Council, Program, Planning and Integration, Brisbane Square, Level 10, 266 George Street, Brisbane, QLD 4000, Australia; (K.F.); (R.T.)
| | - D. İpek Kurtböke
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia; (C.A.); (T.D.T.)
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Adra C, Tran TD, Foster K, Tomlin R, Kurtböke Dİ. Untargeted MS-Based Metabolomic Analysis of Termite Gut-Associated Streptomycetes with Antifungal Activity against Pyrrhoderma noxium. Antibiotics (Basel) 2023; 12:1373. [PMID: 37760670 PMCID: PMC10525753 DOI: 10.3390/antibiotics12091373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Pyrrhoderma noxium is a plant fungal pathogen that induces the disease of brown root rot in a large variety of tree species. It is currently infecting many of the amenity trees within Brisbane City of Queensland, Australia. Steering away from harmful chemical fungicides, biological control agents offer environmentally friendly alternatives. Streptomycetes are known for their production of novel bioactive secondary metabolites with biocontrol potential, particularly, streptomycete symbionts isolated from unique ecological niches. In this study, 37 termite gut-associated actinomycete isolates were identified using molecular methods and screened against P. noxium. A majority of the isolates belonged to the genus Streptomyces, and 15 isolates exhibited strong antifungal activity with up to 98.5% mycelial inhibition of the fungal pathogen. MS/MS molecular networking analysis of the isolates' fermentation extracts revealed several chemical classes with polyketides being among the most abundant. Most of the metabolites, however, did not have matches to the GNPS database, indicating potential novel antifungal compounds in the active extracts obtained from the isolates. Pathway enrichment and overrepresentation analyses revealed pathways relating to polyketide antibiotic production, among other antibiotic pathways, further confirming the biosynthetic potential of the termite gut-associated streptomycetes with biocontrol potential against P. noxium.
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Affiliation(s)
- Cherrihan Adra
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia; (C.A.); (T.D.T.)
| | - Trong D. Tran
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia; (C.A.); (T.D.T.)
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia
| | - Keith Foster
- Brisbane City Council, Program, Planning and Integration, Brisbane Square, Level 10, 266 George Street, Brisbane, QLD 4000, Australia; (K.F.); (R.T.)
| | - Russell Tomlin
- Brisbane City Council, Program, Planning and Integration, Brisbane Square, Level 10, 266 George Street, Brisbane, QLD 4000, Australia; (K.F.); (R.T.)
| | - D. İpek Kurtböke
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD 4558, Australia; (C.A.); (T.D.T.)
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Zhao H, Dai YC, Wu F, Liu XY, Maurice S, Krutovsky KV, Pavlov IN, Lindner DL, Martin FM, Yuan Y. Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia. Genome Biol Evol 2023; 15:evad136. [PMID: 37498334 PMCID: PMC10410303 DOI: 10.1093/gbe/evad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/01/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
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Affiliation(s)
- Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fang Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, George-August University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Department of Genomics and Bioinformatics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, Russia
| | - Igor N Pavlov
- Mycology and Plant Pathology, V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russia
- Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, Russia
| | | | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Champenoux, France
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Shen ZQ, Jiang JH, Li CT, Li Y, Zhou LW. Genome Re-Annotation and Transcriptome Analyses of Sanghuangporus sanghuang. J Fungi (Basel) 2023; 9:jof9050505. [PMID: 37233216 DOI: 10.3390/jof9050505] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 05/27/2023] Open
Abstract
Sanghuangporus sanghuang, the generic type of Sanghuangporus belonging to Hymenochaetaceae, is a precious medicinal wood-inhabiting macrofungus with high commercial potential. To facilitate the medicinal utilization of this fungal resource, transcriptome sequences are newly generated from S. sanghuang strain MS2. In association with the previously generated genome sequences from the same strain by our lab and all available fungal homologous protein sequences in the UniProtKB/Swiss-Prot Protein Sequence Database, a new methodology was employed for genome assembly and annotation. A total of 13,531 protein-coding genes were identified from the new version of the genome of S. sanghuang strain MS2 with a complete BUSCOs of 92.8%, which indicates a remarkable improvement in the accuracy and completeness of the genome assembly. In general, more genes involved in medicinal functions were annotated compared with the original version of the genome annotation, and most of these genes were also found in the transcriptome data of the currently sampled growth period. Given the above, the current genomic and transcriptomic data provides valuable insights into the evolution and metabolites analysis of S. sanghuang.
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Affiliation(s)
- Zi-Qi Shen
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Ministry of Science and Technology, Changchun 130118, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang-Tian Li
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Ministry of Science and Technology, Changchun 130118, China
| | - Yu Li
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Ministry of Science and Technology, Changchun 130118, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Environmental DNA as an innovative technique to identify the origins of falsified antimalarial tablets-a pilot study of the pharmabiome. Sci Rep 2022; 12:21997. [PMID: 36539480 PMCID: PMC9764312 DOI: 10.1038/s41598-022-25196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Falsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines. Medicines may contain diverse adventitious biological contamination, and the sealed nature of blister-packages may capture and preserve genetic signals from the manufacturing processes allowing identification of production source(s). We conducted a blinded pilot study to determine if such environmental DNA (eDNA) could be detected in eleven samples of falsified and genuine artesunate antimalarial tablets, collected in SE Asia, which could be indicative of origin. Massively Parallel Sequencing (MPS) was used to characterize microbial and eukaryote diversity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass samples demonstrated sample specific signals using two target markers. Significant differences in bacterial and eukaryote DNA community structures were observed between genuine and falsified tablets and between different packaging types of falsified artesunate. Human DNA, which was indicative of likely east Asian ancestry, was found in falsified tablets. This pilot study of the 'pharmabiome' shows the potential of environmental DNA as a powerful forensic tool to assist with the identification of the environments, and hence location and timing, of the source and manufacture of falsified medicines, establish links between seizures and complement existing tools to build a more complete picture of criminal trade routes. The finding of human DNA in tablets raises important ethical issues that need to be addressed.
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Kozhar O, Kim M, Ibarra Caballero J, Klopfenstein NB, Cannon PG, Stewart JE. Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia, and the Pacific Islands. Mol Ecol 2022; 31:2013-2031. [DOI: 10.1111/mec.16384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Olga Kozhar
- Colorado State University Fort Collins CO USA
| | - Mee‐Sook Kim
- USDA Forest Service Pacific Northwest Research Station Corvallis OR USA
| | | | | | - Phil G. Cannon
- USDA Forest Service Forest Health Protection Vallejo CA USA
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