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Loreto ES, Tondolo JSM, Zanette RA. Treating Pythiosis with Antibacterial Drugs Targeting Protein Synthesis: An Overview. J Fungi (Basel) 2024; 10:234. [PMID: 38667905 PMCID: PMC11051233 DOI: 10.3390/jof10040234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
This review article explores the effectiveness of antibacterial drugs that inhibit protein synthesis in treating pythiosis, a difficult-to-treat infection caused by Pythium insidiosum. The article highlights the susceptibility of P. insidiosum to antibacterial drugs, such as macrolides, oxazolidinones, and tetracyclines. We examine various studies, including in vitro tests, experimental infection models, and clinical case reports. Based on our synthesis of these findings, we highlight the potential of these drugs in managing pythiosis, primarily when combined with surgical interventions. The review emphasizes the need for personalized treatment strategies and further research to establish standardized testing protocols and optimize therapeutic approaches.
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Affiliation(s)
- Erico S. Loreto
- Sobresp Faculty of Health Sciences, 520 Appel Street, Santa Maria 97015-030, RS, Brazil;
| | - Juliana S. M. Tondolo
- Sobresp Faculty of Health Sciences, 520 Appel Street, Santa Maria 97015-030, RS, Brazil;
| | - Régis A. Zanette
- Department of Pharmacology, Basic Health Sciences Institute, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, Porto Alegre 90035-003, RS, Brazil;
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2
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Verebélyi V, Erdei N, Hardy T, Eszterbauer E. Description of Saprolegnia velencensis sp. n. (Oomycota), a novel water mold species from Lake Velence, Hungary. PLoS One 2024; 19:e0298814. [PMID: 38507310 PMCID: PMC10954141 DOI: 10.1371/journal.pone.0298814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/19/2024] [Indexed: 03/22/2024] Open
Abstract
Here, we describe a novel water mold species, Saprolegnia velencensis sp. n. from Lake Velence, in Hungary. Two strains (SAP239 and SAP241) were isolated from lake water, and characterized using morphological and molecular markers. In addition, phylogenetic analyses based on ITS-rDNA regions and on the RNA polymerase II B subunit (RPB2) gene complemented the study. The ITS-rDNA of the two strains was 100% identical, showed the highest similarity to that of S. ferax (with 94.4% identity), and they formed a separate cluster in both the ITS-rDNA and RPB2-based maximum likelihood phylogenetic trees with high bootstrap support. Although mature oogonia and antheridia were not seen under in vitro conditions, the S. velencensis sp. n. could be clearly distinguished from its closest relative, S. ferax, by the length and width of sporangia, as the new species had shorter and narrower sporangia (163.33±70.07 and 36.69±8.27 μm, respectively) than those of S. ferax. The two species also differed in the size of the secondary cysts (11.63±1.77 μm), which were slightly smaller in S. ferax. Our results showed that S. velencensis sp. n. could not be identified with any of the previously described water mold species, justifying its description as a new species.
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Affiliation(s)
| | - Noémi Erdei
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
| | - Tímea Hardy
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
| | - Edit Eszterbauer
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
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3
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Thimmappa BC, Salhi LN, Forget L, Sarrasin M, Bustamante Villalobos P, Henrissat B, Lang BF, Burger G. A biofertilizing fungal endophyte of cranberry plants suppresses the plant pathogen Diaporthe. Front Microbiol 2024; 15:1327392. [PMID: 38371935 PMCID: PMC10869595 DOI: 10.3389/fmicb.2024.1327392] [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: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
Fungi colonizing plants are gaining attention because of their ability to promote plant growth and suppress pathogens. While most studies focus on endosymbionts from grasses and legumes, the large and diverse group of ericaceous plants has been much neglected. We recently described one of the very few fungal endophytes promoting the growth of the Ericaceae Vaccinium macrocarpon (American cranberry), notably the Codinaeella isolate EC4. Here, we show that EC4 also suppresses fungal pathogens, which makes it a promising endophyte for sustainable cranberry cultivation. By dual-culture assays on agar plates, we tested the potential growth suppression (or biocontrol) of EC4 on other microbes, notably 12 pathogenic fungi and one oomycete reported to infect not only cranberry but also blueberry, strawberry, tomato plants, rose bushes and olive trees. Under greenhouse conditions, EC4 protects cranberry plantlets infected with one of the most notorious cranberry-plant pathogens, Diaporthe vaccinii, known to cause upright dieback and berry rot. The nuclear genome sequence of EC4 revealed a large arsenal of genes potentially involved in biocontrol. About ∼60 distinct clusters of genes are homologs of secondary metabolite gene clusters, some of which were shown in other fungi to synthesize nonribosomal peptides and polyketides, but in most cases, the exact compounds these clusters may produce are unknown. The EC4 genome also encodes numerous homologs of hydrolytic enzymes known to degrade fungal cell walls. About half of the nearly 250 distinct glucanases and chitinases are likely involved in biocontrol because they are predicted to be secreted outside the cell. Transcriptome analysis shows that the expression of about a quarter of the predicted secondary-metabolite gene clusters and glucan and chitin-degrading genes of EC4 is stimulated when it is co-cultured with D. vaccinii. Some of the differentially expressed EC4 genes are alternatively spliced exclusively in the presence of the pathogen, altering the proteins' domain content and subcellular localization signal, thus adding a second level of proteome adaptation in response to habitat competition. To our knowledge, this is the first report of Diaporthe-induced alternative splicing of biocontrol genes.
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Affiliation(s)
- Bhagya C. Thimmappa
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Lila Naouelle Salhi
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Lise Forget
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Matt Sarrasin
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Peniel Bustamante Villalobos
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - B. Franz Lang
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada
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4
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Jeon BS, Park MG. Morphology, phylogeny, and host range of the novel early-diverging oomycete Sirolpidium dinoletiferum sp. nov. parasitizing marine dinoflagellates. HARMFUL ALGAE 2024; 132:102567. [PMID: 38331547 DOI: 10.1016/j.hal.2024.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024]
Abstract
Oomycetes are fungus-like heterotrophic organisms with a broad environmental distribution, including marine, freshwater, and terrestrial habitats. They function as saprotrophs that use the remains of other organisms or as parasites of a variety of eukaryotes, including protists, diatoms, dinoflagellates, macroalgae, plants, fungi, animals, and even other oomycetes. Among the protist hosts, the taxonomy, morphology, and phylogenetic positions of the oomycete parasitoids of diatoms have been well studied; however, this information concerning the oomycete parasitoids of dinoflagellates is poorly understood. During intensive sampling along the east and west coasts of Korea in May and October 2019, a new species of oomycetes was discovered and two strains of the new parasitoid were successfully established in cultures. The new oomycete parasitoid penetrated the dinoflagellate host cell and developed to form a sporangium, which was very similar to the perkinsozoan parasitoids that infect marine dinoflagellates. The most distinctive morphological feature of the new parasitoid was a central large vacuole forming several long discharge tubes. The molecular phylogenetic tree inferred based on the small subunit (SSU) ribosomal DNA (rDNA) revealed that the new parasitoid forms a distinct branch unrelated to other described species belonging to early-diverging oomycetes. It clustered with species belonging to the genus Sirolpidium with strong support values in the cytochrome c oxidase subunit 2 (cox2) tree. Cross-infection experiments showed that infections by the new parasitoid occurred in only six genera belonging to dinoflagellates among the protists tested in this study. Based on the morphological and molecular data obtained in this study, we propose to introduce a new species, Sirolpidium dinoletiferum sp. nov., for this novel parasitoid, conservatively within the genus Sirolpidium.
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Affiliation(s)
- Boo Seong Jeon
- Research Institute for Basic Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju 61186, Korea.
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Yu G, Li W, Yang C, Zhang X, Luo M, Chen T, Wang X, Wang R, Chen Q. PlAtg8-mediated autophagy regulates vegetative growth, sporangial cleavage, and pathogenesis in Peronophythora litchii. Microbiol Spectr 2024; 12:e0353123. [PMID: 38084976 PMCID: PMC10783124 DOI: 10.1128/spectrum.03531-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Peronophythora litchii is the pathogen of litchi downy blight, which is the most serious disease in litchi. Autophagy is an evolutionarily conserved catabolic process in eukaryotes. Atg8 is a core protein of the autophagic pathway, which modulates growth and pathogenicity in the oomycete P. litchii. In P. litchii, CRISPR/Cas9-mediated knockout of the PlATG8 impaired autophagosome formation. PlATG8 knockout mutants exhibited attenuated colony expansion, sporangia production, zoospore discharge, and virulence on litchi leaves and fruits. The reduction in zoospore release was likely underpinned by impaired sporangial cleavage. Thus, in addition to governing autophagic flux, PlAtg8 is indispensable for vegetative growth and infection of P. litchii.
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Affiliation(s)
- Ge Yu
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Wenqiang Li
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Chengdong Yang
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Xue Zhang
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Manfei Luo
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Taixu Chen
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Xuejian Wang
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qinghe Chen
- School of Tropical Agriculture and Forestry, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
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6
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Lin C, Li WJ, Li LJ, Neilson R, An XL, Zhu YG. Movement of protistan trophic groups in soil-plant continuums. Environ Microbiol 2023; 25:2641-2652. [PMID: 37547979 DOI: 10.1111/1462-2920.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil-plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen-consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil-plant continuums, which is fundamental to the regulation of soil-plant microbiomes and maintenance of environmental and human health.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Jing Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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7
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Marcianò D, Toffolatti SL. Methods for Fungicide Efficacy Screenings: Multiwell Testing Procedures for the Oomycetes Phytophthora infestans and Pythium ultimum. Microorganisms 2023; 11:microorganisms11020350. [PMID: 36838315 PMCID: PMC9959339 DOI: 10.3390/microorganisms11020350] [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: 12/05/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Oomycetes-borne diseases represent a serious problem for agriculture sustainability due to the high use of chemical products employed for their control. In recent years, increasing concerns on side effects associated with fungicide utilization have led to the reduction of the permissible modes of action, with the remaining ones continuously threatened by the increase of resistant strains in the pathogen populations. In this context, it is mandatory to develop new generation fungicides characterized by high specificity towards the target species and low environmental impact to guarantee the sustainability, productivity, and quality of food production. Fungicide discovery is a lengthy and costly process, and despite these urgent needs, poor description and formalization of high-throughput methodologies for screening the efficacy of active compounds are commonly reported for these kinds of organisms. In this study, a comprehensive picture of two high-throughput practices for efficient fungicide screening against plant-pathogenic oomycetes has been provided. Different protocols using multiwell plates were validated on approved crop protection products using Phytophthora infestans and Pythium ultimum as the model species. In addition, detailed statistical inputs useful for the analysis of data related to the efficacy of screenings are included.
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8
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Wang H, Xiang Y, Wang D, Fu ZQ. An epic war between an oomycete pathogen and plants. MOLECULAR PLANT 2022; 15:1828-1830. [PMID: 36245121 DOI: 10.1016/j.molp.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Huan Wang
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, and College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Youhuang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, and College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou, China.
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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Cheng Y, Zhang H, Zhu W, Li Q, Meng R, Yang K, Guo Z, Zhai Y, Zhang H, Ji R, Peng H, Dou D, Jing M. Ferroptosis induced by the biocontrol agent Pythium oligandrum enhances soybean resistance to Phytophthora sojae. Environ Microbiol 2022; 24:6267-6278. [PMID: 36250814 DOI: 10.1111/1462-2920.16248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/13/2022] [Indexed: 01/12/2023]
Abstract
Ferroptosis is a newly discovered form of cell death accompanied by iron accumulation and lipid peroxidation. Both biotic and abiotic stresses can induce ferroptosis in plant cells. In the case of plant interactions with pathogenic Phytophthora oomycetes, the roles of ferroptosis are still largely unknown. Here, we performed transcriptome analysis on soybean plants treated with the biocontrol agent Pythium oligandrum, a soilborne and non-pathogenic oomycete capable of inducing plant resistance against Phytophthora sojae infection. Expression of homologous soybean genes involved in ferroptosis and resistance was reprogrammed upon P. oligandrum treatment. Typical hallmarks for characterizing ferroptosis were detected in soybean hypocotyl cells, including decreased glutathione (GSH) level, accumulation of ferric ions, and lipid peroxidation by reactive oxygen species (ROS). Meanwhile, ferroptosis-like cell death was triggered by P. oligandrum to suppress P. sojae infection in soybean. Protection provided by P. oligandrum could be attenuated by the ferroptosis inhibitor ferrostatin-1 (Fer-1), suggesting the critical role of ferroptosis in soybean resistance against P. sojae. Taken together, these results demonstrate that ferroptosis is a P. oligandrum-inducible defence mechanism against oomycete infection in soybean.
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Affiliation(s)
- Yang Cheng
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Huanxin Zhang
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Wenyi Zhu
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Qing Li
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Rui Meng
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Kun Yang
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Ziqian Guo
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Haijing Zhang
- Rongcheng Agricultural and Rural Services Centre, Weihai, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Hao Peng
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Daolong Dou
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Maofeng Jing
- Key Laboratory of Biological Interaction and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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10
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Volynchikova E, Kim KD. Biological Control of Oomycete Soilborne Diseases Caused by Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae in Solanaceous Crops. MYCOBIOLOGY 2022; 50:269-293. [PMID: 36404903 PMCID: PMC9645277 DOI: 10.1080/12298093.2022.2136333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 05/25/2023]
Abstract
Oomycete pathogens that belong to the genus Phytophthora cause devastating diseases in solanaceous crops such as pepper, potato, and tobacco, resulting in crop production losses worldwide. Although the application of fungicides efficiently controls these diseases, it has been shown to trigger negative side effects such as environmental pollution, phytotoxicity, and fungicide resistance in plant pathogens. Therefore, biological control of Phytophthora-induced diseases was proposed as an environmentally sound alternative to conventional chemical control. In this review, progress on biological control of the soilborne oomycete plant pathogens, Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae, infecting pepper, potato, and tobacco is described. Bacterial (e.g., Acinetobacter, Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, and Streptomyces) and fungal (e.g., Trichoderma and arbuscular mycorrhizal fungi) agents, and yeasts (e.g., Aureobasidium, Curvibasidium, and Metschnikowia) have been reported as successful biocontrol agents of Phytophthora pathogens. These microorganisms antagonize Phytophthora spp. via antimicrobial compounds with inhibitory activities against mycelial growth, sporulation, and zoospore germination. They also trigger plant immunity-inducing systemic resistance via several pathways, resulting in enhanced defense responses in their hosts. Along with plant protection, some of the microorganisms promote plant growth, thereby enhancing their beneficial relations with host plants. Although the beneficial effects of the biocontrol microorganisms are acceptable, single applications of antagonistic microorganisms tend to lack consistent efficacy compared with chemical analogues. Therefore, strategies to improve the biocontrol performance of these prominent antagonists are also discussed in this review.
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Affiliation(s)
- Elena Volynchikova
- Laboratory of Plant Disease and Biocontrol, Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea
| | - Ki Deok Kim
- Laboratory of Plant Disease and Biocontrol, Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea
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11
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Myo-D-inositol Trisphosphate Signalling in Oomycetes. Microorganisms 2022; 10:microorganisms10112157. [DOI: 10.3390/microorganisms10112157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Oomycetes are pathogens of plants and animals, which cause billions of dollars of global losses to the agriculture, aquaculture and forestry sectors each year. These organisms superficially resemble fungi, with an archetype being Phytophthora infestans, the cause of late blight of tomatoes and potatoes. Comparison of the physiology of oomycetes with that of other organisms, such as plants and animals, may provide new routes to selectively combat these pathogens. In most eukaryotes, myo-inositol 1,4,5 trisphosphate is a key second messenger that links extracellular stimuli to increases in cytoplasmic Ca2+, to regulate cellular activities. In the work presented in this study, investigation of the molecular components of myo-inositol 1,4,5 trisphosphate signaling in oomycetes has unveiled similarities and differences with that in other eukaryotes. Most striking is that several oomycete species lack detectable phosphoinositide-selective phospholipase C homologues, the enzyme family that generates this second messenger, but still possess relatives of myo-inositol 1,4,5 trisphosphate-gated Ca2+-channels.
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12
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Wang W, Cui T, Zhang F, Xue Z, Zhang B, Liu X. Functional Analysis of the C-5 Sterol Desaturase PcErg3 in the Sterol Auxotrophic Oomycete Pathogen Phytophthora capsici. Front Microbiol 2022; 13:811132. [PMID: 35651492 PMCID: PMC9151008 DOI: 10.3389/fmicb.2022.811132] [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] [Received: 11/08/2021] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
Although sterols play an important role in most eukaryotes, some oomycetes, including Phytophthora spp., have lost the sterol synthesis pathway. Nevertheless, the ERG3 gene encoding C-5 sterol desaturase in the sterol synthesis pathway is still present in the genomes of Phytophthora spp. Phytophthora capsici, a destructive pathogen with a broad range of plant hosts, poses a significant threat to the production of agriculture. This study focused on the ERG3 gene in P. capsici (PcERG3) and explored its function in this pathogen. It showed that the PcERG3 gene could be expressed in all tested developmental stages of P. capsici, with sporangium and mycelium displaying higher expression levels. A potential substrate of Erg3 (stellasterol) was used to treat the P. capsici wild-type strain and a PcERG3Δ transformant, and their sterol profiles were determined by GC-MS. The wild-type strain could convert stellasterol into the down-stream product while the transformant could not, indicating that PcErg3 retains the C-5 sterol desaturase activity. By comparing the biological characteristics of different strains, it was found that PcERG3 is not important for the development of P. capsici. The pathogenicity of the PcERG3Δ transformants and the wild-type strain was comparable, suggesting that PcERG3 is not necessary for the interaction between P. capsici and its hosts. Further investigations revealed that the PcERG3Δ transformants and the wild-type strain displayed a similar level of tolerance to external adversities such as unsuitable temperatures, high osmotic pressures, and intemperate pH, signifying that PcERG3 is not essential for P. capsici to cope with these environmental stresses.
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Affiliation(s)
- Weizhen Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Tongshan Cui
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Fan Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhaolin Xue
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Borui Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xili Liu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
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13
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Pythium oligandrum in plant protection and growth promotion: Secretion of hydrolytic enzymes, elicitors and tryptamine as auxin precursor. Microbiol Res 2022; 258:126976. [DOI: 10.1016/j.micres.2022.126976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/25/2022]
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14
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Li W, Li P, Zhou X, Situ J, Lin Y, Qiu J, Yuan Y, Xi P, Jiang Z, Kong G. A Cytochrome B 5-Like Heme/Steroid Binding Domain Protein, PlCB5L1, Regulates Mycelial Growth, Pathogenicity and Oxidative Stress Tolerance in Peronophythora litchii. FRONTIERS IN PLANT SCIENCE 2021; 12:783438. [PMID: 34899811 PMCID: PMC8655872 DOI: 10.3389/fpls.2021.783438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
As an electron transport component, cytochrome b5 is an essential component of the Class II cytochrome P450 monooxygenation system and widely present in animals, plants, and fungi. However, the roles of Cyt-b5 domain proteins in pathogenic oomycetes remain unknown. Peronophythora litchii is an oomycete pathogen that causes litchi downy blight, the most destructive disease of litchi. In this study, we identified a gene, designated PlCB5L1, that encodes a Cyt-b5 domain protein in P. litchii, and characterized its function. PlCB5L1 is highly expressed in the zoospores, cysts, germinated cysts, and during early stages of infection. PlCB5L1 knockout mutants showed reduced growth rate and β-sitosterol utilization. Importantly, we also found that PlCB5L1 is required for the full pathogenicity of P. litchii. Compared with the wild-type strain, the PlCB5L1 mutants exhibited significantly higher tolerance to SDS and sorbitol, but impaired tolerance to cell wall stress, osmotic stress, and oxidative stress. Further, the expression of genes involved in oxidative stress tolerance, including peroxidase, cytochrome P450, and laccase genes, were down-regulated in PlCB5L1 mutants under oxidative stress. This is the first report that a Cyt-b5 domain protein contributes to the development, stress response, and pathogenicity in plant pathogenic oomycetes.
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Affiliation(s)
- Wen Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Peng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Junjian Situ
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Yiming Lin
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Jiahui Qiu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Yuling Yuan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Pinggen Xi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Zide Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Guanghui Kong
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
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15
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Kaczmarek A, Boguś MI. Fungi of entomopathogenic potential in Chytridiomycota and Blastocladiomycota, and in fungal allies of the Oomycota and Microsporidia. IMA Fungus 2021; 12:29. [PMID: 34635188 PMCID: PMC8504053 DOI: 10.1186/s43008-021-00074-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/25/2021] [Indexed: 11/10/2022] Open
Abstract
The relationship between entomopathogenic fungi and their insect hosts is a classic example of the co-evolutionary arms race between pathogen and target host. The present review describes the entomopathogenic potential of Chytridiomycota and Blastocladiomycota fungi, and two groups of fungal allies: Oomycota and Microsporidia. The Oomycota (water moulds) are considered as a model biological control agent of mosquito larvae. Due to their shared ecological and morphological similarities, they had long been considered a part of the fungal kingdom; however, phylogenetic studies have since placed this group within the Straminipila. The Microsporidia are parasites of economically-important insects, including grasshoppers, lady beetles, bumblebees, colorado potato beetles and honeybees. They have been found to display some fungal characteristics, and phylogenetic studies suggest that they are related to fungi, either as a basal branch or sister group. The Blastocladiomycota and Chytridiomycota, named the lower fungi, historically were described together; however, molecular phylogenetic and ultrastructural research has classified them in their own phylum. They are considered parasites of ants, and of the larval stages of black flies, mosquitoes and scale insects.
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Affiliation(s)
- Agata Kaczmarek
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland.
| | - Mieczysława I Boguś
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
- Biomibo, Strzygłowska 15, 04-872, Warsaw, Poland
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16
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Tang J, Gu X, Liu J, He Z. Roles of small RNAs in crop disease resistance. STRESS BIOLOGY 2021; 1:6. [PMID: 37676520 PMCID: PMC10429495 DOI: 10.1007/s44154-021-00005-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/19/2021] [Indexed: 09/08/2023]
Abstract
Small RNAs (sRNAs) are a class of short, non-coding regulatory RNAs that have emerged as critical components of defense regulatory networks across plant kingdoms. Many sRNA-based technologies, such as host-induced gene silencing (HIGS), spray-induced gene silencing (SIGS), virus-induced gene silencing (VIGS), artificial microRNA (amiRNA) and synthetic trans-acting siRNA (syn-tasiRNA)-mediated RNA interference (RNAi), have been developed as disease control strategies in both monocot and dicot plants, particularly in crops. This review aims to highlight our current understanding of the roles of sRNAs including miRNAs, heterochromatic siRNAs (hc-siRNAs), phased, secondary siRNAs (phasiRNAs) and natural antisense siRNAs (nat-siRNAs) in disease resistance, and sRNAs-mediated trade-offs between defense and growth in crops. In particular, we focus on the diverse functions of sRNAs in defense responses to bacterial and fungal pathogens, oomycete and virus in crops. Further, we highlight the application of sRNA-based technologies in protecting crops from pathogens. Further research perspectives are proposed to develop new sRNAs-based efficient strategies to breed non-genetically modified (GMO), disease-tolerant crops for sustainable agriculture.
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Affiliation(s)
- Jun Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueting Gu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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17
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Mazel F, Malard L, Niculita-Hirzel H, Yashiro E, Mod HK, Mitchell EAD, Singer D, Buri A, Pinto E, Guex N, Lara E, Guisan A. Soil protist function varies with elevation in the Swiss Alps. Environ Microbiol 2021; 24:1689-1702. [PMID: 34347350 PMCID: PMC9290697 DOI: 10.1111/1462-2920.15686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Erika Yashiro
- Center for Microbial Communities, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, CH-2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Pinto
- Terrabiom Association, Dörflistrasse 32, Oberrieden, Zürich, 8942, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
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18
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de Vries S, de Vries J. A Global Survey of Carbohydrate Esterase Families 1 and 10 in Oomycetes. Front Genet 2020; 11:756. [PMID: 32849784 PMCID: PMC7427535 DOI: 10.3389/fgene.2020.00756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022] Open
Abstract
Carbohydrate-active enzymes (CAZymes) are a cornerstone in the phytopathogenicity of filamentous microbes. CAZymes are required for every step of a successful infection cycle-from penetration, to nutrient acquisition (during colonization), to exit and dispersal. Yet, CAZymes are not a unique feature of filamentous pathogens. They are found across eukaryotic genomes and including, for example, saprotrophic relatives of major pathogens. Comparative genomics and functional analyses revealed that CAZyme content is shaped by a multitude of factors, including utilized substrate, lifestyle, and host preference. Yet, family size alone says little about usage. Indeed, in a previous study, we found that genes putatively coding for the CAZyme families of carbohydrate esterase (CE)1 and CE10, while not specifically enriched in number, were suggested to have lifestyle-specific gene expression patterns. Here, we used comparative genomics and a clustering approach to understand how the repertoire of the CE1- and CE10-encoding gene families is shaped across oomycete evolution. These data are combined with comparative transcriptomic analyses across homologous clusters within the gene families. We find that CE1 and CE10 have been reduced in number in biotrophic oomycetes independent of the phylogenetic relationship of the biotrophs to each other. The reduction in CE1 is different from that observed for CE10: While in CE10 specific clusters of homologous sequences show convergent reduction, CE1 reduction is caused by species-specific losses. Comparative transcriptomics revealed that some clusters of CE1 or CE10 sequences have a higher expression than others, independent of the species composition within them. Further, we find that CE1- and CE10-encoding genes are mainly induced in plant pathogens and that some homologous genes show lifestyle-specific gene expression levels during infection, with hemibiotrophs showing the highest expression levels.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göettingen, Göettingen, Germany
- Göettingen Center for Molecular Biosciences (GZMB), University of Göettingen, Göettingen, Germany
- Campus Institute Data Science, University of Göettingen, Göettingen, Germany
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19
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Dupeyron M, Baril T, Bass C, Hayward A. Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. Mob DNA 2020; 11:21. [PMID: 32612713 PMCID: PMC7325037 DOI: 10.1186/s13100-020-00212-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/08/2020] [Indexed: 01/18/2023] Open
Abstract
Background Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity. Results We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily. Conclusions Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.
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Affiliation(s)
- Mathilde Dupeyron
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
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20
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Guo D, Yuan C, Luo Y, Chen Y, Lu M, Chen G, Ren G, Cui C, Zhang J, An D. Biocontrol of tobacco black shank disease (Phytophthora nicotianae) by Bacillus velezensis Ba168. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 165:104523. [PMID: 32359551 DOI: 10.1016/j.pestbp.2020.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 06/11/2023]
Abstract
Tobacco black shank (TBS) caused by Phytophthora nicotianae is destructive to almost all tobacco cultivars and is widespread in many tobacco-growing countries. Through lab study and field test, we isolated plant growth-promoting rhizobacteria (PGPR) strain Ba168 which is a promising biocontrol strain of TBS. Ba168 was isolated from 168 soil samples and identified as Bacillus velezensis by its genetic and phenotypic characteristics. A susceptibility test indicated that the P. nicotianae antagonistic materials of Ba168 in extracellular metabolites were composed of effective and stable proteins/peptides. P. nicotianae's growth was suppressed by the ammonium sulfate precipitation of Ba168 culture filtrates (ASPBa) at a minimum inhibitory concentration of 5 μg/mL. Extracellular conductivity, pH, and the wet/dry weights of P. nicotianae's mycelia, along with scanning electron microscope analysis, suggested that Ba168-derived proteins/peptides could effectively inhibit P. nicotianae by causing irreversible damage to its cell walls and membranes. Protein identification of ASPBa supported these results and identified many key proteins responsible for various biocontrol-related pathways. Field assays of TBS control efficacy of many PGPRs and agrochemicals showed that all PGPR preparations reduced the disease index of tobacco, but Ba168 was the most effective. These results demonstrated the importance of Bacillus-derived proteins/peptides in the inhibition of P. nicotianae through irreversible damage to its cell wall and membrane; and the effectiveness of PGPR strain B. velezensis Ba168 for biocontrol of the soil-borne disease caused by P. nicotianae.
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Affiliation(s)
- Dongsheng Guo
- College of Plant Protection and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenhong Yuan
- College of Plant Protection and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunyan Luo
- College of Plant Protection and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - YaHan Chen
- College of Plant Protection and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meihuan Lu
- College of Plant Protection and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guochan Chen
- Henan Academy of Sciences Institute of Biology, Limited Liability Company, Zhenzhou, Henan 450000, China
| | - Guangwei Ren
- Tobacco Research Institute of CAAS, Qingzhou, Shandong 262500,China
| | - Chuanbin Cui
- Shaanxi Tobacco Scientific Institution, Xian, Shaanxi 710000, China
| | - Jiatao Zhang
- Shaanxi Tobacco Scientific Institution, Xian, Shaanxi 710000, China
| | - Derong An
- College of Plant Protection and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China.
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21
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Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum. G3-GENES GENOMES GENETICS 2020; 10:431-436. [PMID: 31792008 PMCID: PMC7003069 DOI: 10.1534/g3.119.400746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pythium oligandrum is a soil born free living oomycete able to parasitize fungi and oomycetes prey, including important plant and animals pathogens. Pythium oligandrum can colonize endophytically the root tissues of diverse plants where it induces plant defenses. Here we report the first long-read genome sequencing of a P. oligandrum strain sequenced by PacBio technology. Sequencing of genomic DNA loaded onto six SMRT cells permitted the acquisition of 913,728 total reads resulting in 112X genome coverage. The assembly and polishing of the genome sequence yielded180 contigs (N50 = 1.3 Mb; L50 = 12). The size of the genome assembly is 41.9 Mb with a longest contig of 2.7 Mb and 15,007 predicted protein-coding genes among which 95.25% were supported by RNAseq data, thus constituting a new Pythium genome reference. This data will facilitate genomic comparisons of Pythium species that are commensal, beneficial or pathogenic on plant, or parasitic on fungi and oomycete to identify key genetic determinants underpinning their diverse lifestyles. In addition comparison with plant pathogenic or zoopathogenic species will illuminate genomic adaptations for pathogenesis toward widely diverse hosts.
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22
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Hassett BT, Thines M, Buaya A, Ploch S, Gradinger R. A glimpse into the biogeography, seasonality, and ecological functions of arctic marine Oomycota. IMA Fungus 2019; 10:6. [PMID: 32647615 PMCID: PMC7325649 DOI: 10.1186/s43008-019-0006-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 02/05/2023] Open
Abstract
High-latitude environments are warming, leading to changes in biological diversity patterns of taxa. Oomycota are a group of fungal-like organisms that comprise a major clade of eukaryotic life and are parasites of fish, agricultural crops, and algae. The diversity, functionality, and distribution of these organisms are essentially unknown in the Arctic marine environment. Thus, it was our aim to conduct a first screening, using a functional gene assay and high-throughput sequencing of two gene regions within the 18S rRNA locus to examine the diversity, richness, and phylogeny of marine Oomycota within Arctic sediment, seawater, and sea ice. We detected Oomycota at every site sampled and identified regionally localized taxa, as well as taxa that existed in both Alaska and Svalbard. While the recently described diatom parasite Miracula helgolandica made up about 50% of the oomycete reads found, many lineages were observed that could not be assigned to known species, including several that clustered with another recently described diatom parasite, Olpidiopsis drebesii. Across the Arctic, Oomycota comprised a maximum of 6% of the entire eukaryotic microbial community in Barrow, Alaska May sediment and 10% in sea ice near the Svalbard archipelago. We found Arctic marine Oomycota encode numerous genes involved in parasitism and carbon cycling processes. Ultimately, these data suggest that Arctic marine Oomycota are a reservoir of uncharacterized biodiversity, the majority of which are probably parasites of diatoms, while others might cryptically cycle carbon or interface other unknown ecological processes. As the Arctic continues to warm, lower-latitude Oomycota might migrate into the Arctic Ocean and parasitize non-coevolved hosts, leading to incalculable shifts in the primary producer community.
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Affiliation(s)
- Brandon T Hassett
- UiT-Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019 Tromsø, Norway
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60435 Frankfurt am Main, Germany.,Translational Biodiversity Genomics Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Anthony Buaya
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60435 Frankfurt am Main, Germany
| | - Sebastian Ploch
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - R Gradinger
- UiT-Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019 Tromsø, Norway
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