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Sheikh TMM, Chen J, Wang L, Zhou D, Deng S, Velasco de Castro Oliveira J, Raza W, Wei L, Daly P. Applications of Pythium- and Phytophthora-produced volatiles in plant disease control. Appl Microbiol Biotechnol 2024; 108:479. [PMID: 39361130 PMCID: PMC11450046 DOI: 10.1007/s00253-024-13312-1] [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: 07/03/2024] [Revised: 09/13/2024] [Accepted: 09/16/2024] [Indexed: 10/06/2024]
Abstract
Volatile organic compounds (VOCs) mediate biological interactions and are produced by Pythium and Phytophthora species. These VOCs are biotechnologically relevant because the genera include important plant pathogens, whereby VOCs can aid in disease detection, and biological control agents, whereby VOCs contribute to disease control. Studies on VOC production, identification, and characterization of individual VOCs produced by Pythium and Phytophthora species are reviewed. VOCs detected in plants infected with Phytophthora species are also reviewed as potentially oomycete-derived VOCs. The Pythium- and Phytophthora-produced VOCs are compared with other microorganisms, and the main effects of these VOCs on microbial inhibition and plant-mediated effects are reviewed. These effects are summarized from direct demonstration studies and inferences based on the known functions of the identified Pythium- and Phytophthora-produced VOCs. There are two main applications of VOCs to plant disease control: the use of VOCs to detect pathogenic Pythium and Phytophthora species, e.g., e-nose detecting systems, and the use of VOC-producing biological control agents, e.g., Pythium oligandrum. Future research could understand how the VOCs are produced to engineer VOC levels in strains, analyze more oomycete species and strains, accurately quantify the VOCs produced, and exploit recent developments in analytical chemistry technology. KEY POINTS: • Compiled inventory of volatiles produced by Phytophthora and Pythium species • Volatilomes contain microbe-inhibiting and plant growth-promoting compounds • Volatile potential in disease detection and control supports analyzing more species.
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Affiliation(s)
- Taha Majid Mahmood Sheikh
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 50 Zhongling St, Nanjing, 210014, China
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
| | - Jinhao Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan, China
| | - Lunji Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan, China
| | - Dongmei Zhou
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 50 Zhongling St, Nanjing, 210014, China
| | - Sheng Deng
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 50 Zhongling St, Nanjing, 210014, China
| | | | - Waseem Raza
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Lihui Wei
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 50 Zhongling St, Nanjing, 210014, China.
| | - Paul Daly
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 50 Zhongling St, Nanjing, 210014, China.
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Ćirković J, Radojković AM, Jovanović J, Perać S, Branković ZM, Milenković I, Milanović SD, Dobrosavljević JN, Tadić VM, Žugić AR, Branković G. Encapsulated Thuja plicata essential oil into biopolymer matrix as a potential pesticide against Phytophthora root pathogens. Int J Biol Macromol 2024; 278:134684. [PMID: 39214830 DOI: 10.1016/j.ijbiomac.2024.134684] [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: 04/30/2024] [Revised: 07/30/2024] [Accepted: 08/10/2024] [Indexed: 09/04/2024]
Abstract
A new formulation that gradually released encapsulated Thuja plicata essential oil (TPEO) as an active component from a biopolymer matrix within a given period was obtained. Antimicrobial activity was determined in in-vitro tests where pure TPEO successfully inhibited the development of different Phytophthora species. The TPEO essential oil was encapsulated into the biopolymer matrix and an oil-in-water emulsion was formed. FTIR spectra analysis confirmed the formation of electrostatic interaction between these polymers, and hydrogen interactions between active components of TPEO and polymer chains. The stability of the emulsions was confirmed by zeta potential measurements, with a value of about 30 mV, even after 14 days of aging. UV-Vis spectra analysis revealed that >60 % of TPEO remained in the emulsion after 14 days of exposure to ambient conditions, whereas pure TPEO evaporated faster, and around 20 % remained after 6 days. Encapsulated TPEO almost completely inhibited the growth of Phytophthora species during the ten-day day's exposition being statistically significantly improved compared to fungicide treatment. It was demonstrated that the emulsion exhibited a prolonged antimicrobial effect and successfully suppressed the growth of Phytophthora species, and can be considered as a means of protection in forests and crops.
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Affiliation(s)
- Jovana Ćirković
- University of Belgrade, Institute for Multidisciplinary Research, KnezaVišeslava 1, 11030 Belgrade, Serbia.
| | - Aleksandar M Radojković
- University of Belgrade, Institute for Multidisciplinary Research, KnezaVišeslava 1, 11030 Belgrade, Serbia; Center of Excellence for Green Technologies, University of Belgrade, Institute for Multidisciplinary Research, 11030 Belgrade, Serbia
| | - Jelena Jovanović
- University of Belgrade, Institute for Multidisciplinary Research, KnezaVišeslava 1, 11030 Belgrade, Serbia; Center of Excellence for Green Technologies, University of Belgrade, Institute for Multidisciplinary Research, 11030 Belgrade, Serbia
| | - Sanja Perać
- University of Belgrade, Institute for Multidisciplinary Research, KnezaVišeslava 1, 11030 Belgrade, Serbia
| | - Zorica M Branković
- University of Belgrade, Institute for Multidisciplinary Research, KnezaVišeslava 1, 11030 Belgrade, Serbia; Center of Excellence for Green Technologies, University of Belgrade, Institute for Multidisciplinary Research, 11030 Belgrade, Serbia
| | - Ivan Milenković
- University of Belgrade, Faculty of Forestry, KnezaVišeslava 1, 11030, Serbia; Mendel University in Brno, Faculty of Forestry and Wood Technology, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Slobodan D Milanović
- University of Belgrade, Faculty of Forestry, KnezaVišeslava 1, 11030, Serbia; Mendel University in Brno, Faculty of Forestry and Wood Technology, Zemědělská 3, 613 00 Brno, Czech Republic
| | | | - Vanja M Tadić
- Institute for Medicinal Plant Research "Dr Josif Pančić", Tadeuša Košćuška 1, 11000 Belgrade, Serbia
| | - Ana R Žugić
- Institute for Medicinal Plant Research "Dr Josif Pančić", Tadeuša Košćuška 1, 11000 Belgrade, Serbia
| | - Goran Branković
- University of Belgrade, Institute for Multidisciplinary Research, KnezaVišeslava 1, 11030 Belgrade, Serbia; Center of Excellence for Green Technologies, University of Belgrade, Institute for Multidisciplinary Research, 11030 Belgrade, Serbia
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3
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Dort EN, Hamelin RC. Heterogeneity in establishment of polyethylene glycol-mediated plasmid transformations for five forest pathogenic Phytophthora species. PLoS One 2024; 19:e0306158. [PMID: 39255283 PMCID: PMC11386421 DOI: 10.1371/journal.pone.0306158] [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: 06/11/2024] [Accepted: 08/26/2024] [Indexed: 09/12/2024] Open
Abstract
Plasmid-mediated DNA transformation is a foundational molecular technique and the basis for most CRISPR-Cas9 gene editing systems. While plasmid transformations are well established for many agricultural Phytophthora pathogens, development of this technique in forest Phytophthoras is lacking. Given our long-term research objective to develop CRISPR-Cas9 gene editing in a forest pathogenic Phytophthora species, we sought to establish the functionality of polyethylene glycol (PEG)-mediated plasmid transformation in five species: P. cactorum, P. cinnamomi, P. cryptogea, P. ramorum, and P. syringae. We used the agricultural pathogen P. sojae, a species for which PEG-mediated transformations are well-established, as a transformation control. Using a protocol previously optimized for P. sojae, we tested transformations in the five forest Phytophthoras with three different plasmids: two developed for CRISPR-Cas9 gene editing and one developed for fluorescent protein tagging. Out of the five species tested, successful transformation, as indicated by stable growth of transformants on a high concentration of antibiotic selective growth medium and diagnostic PCR, was achieved only with P. cactorum and P. ramorum. However, while transformations in P. cactorum were consistent and stable, transformations in P. ramorum were highly variable and yielded transformants with very weak mycelial growth and abnormal morphology. Our results indicate that P. cactorum is the best candidate to move forward with CRISPR-Cas9 protocol development and provide insight for future optimization of plasmid transformations in forest Phytophthoras.
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Affiliation(s)
- Erika N Dort
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard C Hamelin
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec City, Québec, Canada
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Kharel A, Rookes J, Ziemann M, Cahill D. Viable protoplast isolation, organelle visualization and transformation of the globally distributed plant pathogen Phytophthora cinnamomi. PROTOPLASMA 2024; 261:1073-1092. [PMID: 38702562 PMCID: PMC11358197 DOI: 10.1007/s00709-024-01953-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/11/2024] [Indexed: 05/06/2024]
Abstract
Phytophthora cinnamomi is an oomycete plant pathogen with a host range of almost 5000 plant species worldwide and therefore poses a serious threat to biodiversity. Omics technology has provided significant progress in our understanding of oomycete biology, however, transformation studies of Phytophthora for gene functionalisation are still in their infancy. Only a limited number of Phytophthora species have been successfully transformed and gene edited to elucidate the role of particular genes. There is a need to escalate our efforts to understand molecular processes, gene regulation and infection mechanisms of the pathogen to enable us to develop new disease management strategies. The primary obstacle hindering the advancement of transformation studies in Phytophthora is their challenging and unique nature, coupled with our limited comprehension of why they remain such an intractable system to work with. In this study, we have identified some of the key factors associated with the recalcitrant nature of P. cinnamomi. We have incorporated fluorescence microscopy and flow cytometry along with the organelle-specific dyes, fluorescein diacetate, Hoechst 33342 and MitoTracker™ Red CMXRos, to assess P. cinnamomi-derived protoplast populations. This approach has also provided valuable insights into the broader cell biology of Phytophthora. Furthermore, we have optimized the crucial steps that allow transformation of P. cinnamomi and have generated transformed isolates that express a cyan fluorescent protein, with a transformation efficiency of 19.5%. We therefore provide a platform for these methodologies to be applied for the transformation of other Phytophthora species and pave the way for future gene functionalisation studies.
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Affiliation(s)
- Aayushree Kharel
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, VIC, 3216, Australia
| | - James Rookes
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, VIC, 3216, Australia
| | - Mark Ziemann
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, VIC, 3216, Australia
- Burnet Institute, Melbourne, Australia
| | - David Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, VIC, 3216, Australia.
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5
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Coles DW, Bithell SL, Jeffries T, Cuddy WS, Plett JM. Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis. FRONTIERS IN PLANT SCIENCE 2024; 15:1439020. [PMID: 39224851 PMCID: PMC11366588 DOI: 10.3389/fpls.2024.1439020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024]
Abstract
Introduction Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis. Methods To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analyzed the transcriptome of P. medicaginis across three phases of colonization of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem. Results The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterization of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death. Discussion These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.
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Affiliation(s)
- Donovin W. Coles
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Sean L. Bithell
- New South Wales Department of Primary Industries, Tamworth, NSW, Australia
| | - Thomas Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - William S. Cuddy
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Jonathan M. Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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Guan Y, Gajewska J, Floryszak‐Wieczorek J, Tanwar UK, Sobieszczuk‐Nowicka E, Arasimowicz‐Jelonek M. Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology. MOLECULAR PLANT PATHOLOGY 2024; 25:e13497. [PMID: 39034655 PMCID: PMC11261156 DOI: 10.1111/mpp.13497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/21/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024]
Abstract
Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.
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Affiliation(s)
- Yufeng Guan
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Joanna Gajewska
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | | | - Umesh Kumar Tanwar
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Ewa Sobieszczuk‐Nowicka
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Magdalena Arasimowicz‐Jelonek
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
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7
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Charron G, Yergeau J, Van der Heyden H, Bilodeau GJ, Beaulieu C, Tanguay P. Survey of Phytophthora Diversity Reveals P. abietivora as a Potential Phytophthora Root Rot Pathogen in Québec Christmas Tree Plantations. PLANT DISEASE 2024; 108:1445-1454. [PMID: 38127638 DOI: 10.1094/pdis-12-23-2670-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Christmas trees are an economically and culturally important ornamental plant in North America. Many microorganisms are pathogens of firs cultivated as Christmas trees. Among those, Phytophthora causes millions of dollars in damage to plantations annually. In Canada, it is unknown which species are responsible for Phytophthora root rot (PRR) of cultivated Abies species. Between 2019 and 2021, soil and root samples were collected from 40 Christmas tree plantations in Québec province. We used soil baiting and direct isolation from unidentified root fragments to assess the diversity of culturable Phytophthora spp. The obtained isolates were identified using a multilocus sequencing and phylogenetic approach. A total of 44 isolates were identified, including eight P. chlamydospora, eight P. abietivora, seven P. gonapodyides, three P. gregata, six P. megasperma, and two P. kelmanii isolates, plus 10 isolates belonging to a previously unknown taxon that is phylogenetically close to P. chlamydospora and P. gonapodyides. Among the known species, P. abietivora was the most prevalent isolated species associated with trees showing aboveground PRR-like symptoms. Pathogenicity trials confirmed the pathogenicity potential of P. abietivora on both Fraser fir and balsam fir seedlings. Our study provides a first snapshot of the Phytophthora diversity in Québec's Christmas tree productions and describes multiple potential first associations between Phytophthora species and Abies balsamea and A. fraseri.[Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Guillaume Charron
- Natural Resources Canada, Laurentian Forestry Centre, Québec, Québec G1V 4C7, Canada
- Phytodata, Sherrington, Québec J0L 2N0, Canada
| | - Julie Yergeau
- Natural Resources Canada, Laurentian Forestry Centre, Québec, Québec G1V 4C7, Canada
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | | | | | - Carole Beaulieu
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Philippe Tanguay
- Natural Resources Canada, Laurentian Forestry Centre, Québec, Québec G1V 4C7, Canada
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Qian H, Lin L, Zhang Z, Gu X, Shen D, Yin Z, Ye W, Dou D, Wang Y. A MYB-related transcription factor regulates effector gene expression in an oomycete pathogen. MOLECULAR PLANT PATHOLOGY 2024; 25:e13468. [PMID: 38808392 PMCID: PMC11134190 DOI: 10.1111/mpp.13468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Phytophthora pathogens possess hundreds of effector genes that exhibit diverse expression patterns during infection, yet how the expression of effector genes is precisely regulated remains largely elusive. Previous studies have identified a few potential conserved transcription factor binding sites (TFBSs) in the promoters of Phytophthora effector genes. Here, we report a MYB-related protein, PsMyb37, in Phytophthora sojae, the major causal agent of root and stem rot in soybean. Yeast one-hybrid and electrophoretic mobility shift assays showed that PsMyb37 binds to the TACATGTA motif, the most prevalent TFBS in effector gene promoters. The knockout mutant of PsMyb37 exhibited significantly reduced virulence on soybean and was more sensitive to oxidative stress. Consistently, transcriptome analysis showed that numerous effector genes associated with suppressing plant immunity or scavenging reactive oxygen species were down-regulated in the PsMyb37 knockout mutant during infection compared to the wild-type P. sojae. Several promoters of effector genes were confirmed to drive the expression of luciferase in a reporter assay. These results demonstrate that a MYB-related transcription factor contributes to the expression of effector genes in P. sojae.
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Affiliation(s)
- Hui Qian
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Long Lin
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Zhichao Zhang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Xinyi Gu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Danyu Shen
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Zhiyuan Yin
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Wenwu Ye
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Daolong Dou
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
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Christova PK. Phytophthora polonica and Phytophthora hydropathica from Clade 9 Associated with Alder Decline in Bulgaria. Life (Basel) 2024; 14:720. [PMID: 38929703 PMCID: PMC11205215 DOI: 10.3390/life14060720] [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: 04/18/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
A number of Phytophthora species have been identified as destructive plant pathogens and invasive species. They have the potential to affect a wide range of host plants and cause diseases in agricultural and forest ecosystems. Two Phytophthora species from rhizosphere soil samples collected from declining Alnus glutinosa in Bulgaria were isolated in the autumn of 2022. They were identified as Phytophthora polonica and Phytophthora hydropathica according to the DNA sequence analysis of the ITS region, as well as their morphological and physiological characteristics. The pathogenicity of both species to common and gray alder was evaluated by the inoculation of detached leaves and cuttings. Experimental data proved that P. polonica and P. hydropathica are able to cause leaf necrosis not only on A. glutinosa from which they were derived, but also on A. incana. No significant deference in the aggressiveness of the studied isolates from both Phytophthora species against the two tested plants was observed. Therefore, P. polonica and P. hydropathica were determined as potential threats for alder ecosystems in the country. This is the first report for the isolation of P. polonica in Bulgaria and represents the most southeastern point of the species distribution in Europe.
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Affiliation(s)
- Petya Koeva Christova
- AgroBioInstitute, Agricultural Academy, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
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10
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Gomes Marques I, Vieites-Blanco C, Rodríguez-González PM, Segurado P, Marques M, Barrento MJ, Fernandes MR, Cupertino A, Almeida H, Biurrun I, Corcobado T, Costa E Silva F, Díez JJ, Dufour S, Faria C, Ferreira MT, Ferreira V, Jansson R, Machado H, Marçais B, Moreira AC, Oliva J, Pielech R, Rodrigues AP, David TS, Solla A, Jung T. The ADnet Bayesian belief network for alder decline: Integrating empirical data and expert knowledge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:173619. [PMID: 38825208 DOI: 10.1016/j.scitotenv.2024.173619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/03/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024]
Abstract
The globalization in plant material trading has caused the emergence of invasive pests in many ecosystems, such as the alder pathogen Phytophthora ×alni in European riparian forests. Due to the ecological importance of alder to the functioning of rivers and the increasing incidence of P. ×alni-induced alder decline, effective and accessible decision tools are required to help managers and stakeholders control the disease. This study proposes a Bayesian belief network methodology to integrate diverse information on the factors affecting the survival and infection ability of P. ×alni in riparian habitats to help predict and manage disease incidence. The resulting Alder Decline Network (ADnet) management tool integrates information about alder decline from scientific literature, expert knowledge and empirical data. Expert knowledge was gathered through elicitation techniques that included 19 experts from 12 institutions and 8 countries. An original dataset was created covering 1189 European locations, from which P. ×alni occurrence was modeled based on bioclimatic variables. ADnet uncertainty was evaluated through its sensitivity to changes in states and three scenario analyses. The ADnet tool indicated that mild temperatures and high precipitation are key factors favoring pathogen survival. Flood timing, water velocity, and soil type have the strongest influence on disease incidence. ADnet can support ecosystem management decisions and knowledge transfer to address P. ×alni-induced alder decline at local or regional levels across Europe. Management actions such as avoiding the planting of potentially infected trees or removing man-made structures that increase the flooding period in disease-affected sites could decrease the incidence of alder disease in riparian forests and limit its spread. The coverage of the ADnet tool can be expanded by updating data on the pathogen's occurrence, particularly from its distributional limits. Research on the role of genetic variability in alder susceptibility and pathogen virulence may also help improve future ADnet versions.
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Affiliation(s)
- Inês Gomes Marques
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal; cE3c - Center for Ecology, Evolution and Environmental Change & CHANGE - Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Cristina Vieites-Blanco
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Patricia M Rodríguez-González
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal.
| | - Pedro Segurado
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Marlene Marques
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Maria J Barrento
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Maria R Fernandes
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Arthur Cupertino
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Helena Almeida
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Idoia Biurrun
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Apdo. 644, 48080 Bilbao, Spain
| | - Tamara Corcobado
- Austrian Research Centre for Forests (BFW), Vienna, Austria; Phytophthora Research Centre, Mendel University, 613 00 Brno, Czech Republic
| | - Filipe Costa E Silva
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Julio J Díez
- iuFOR- Sustainable Forest Management, Research Institute, University of Valladolid, 34004 Palencia, Spain
| | - Simon Dufour
- Université Rennes 2, CNRS, UMR LETG, CA 24307-35043 Rennes Cedex, France
| | - Carla Faria
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Maria T Ferreira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Verónica Ferreira
- MARE - Marine and Environmental Sciences Centre, ARNET - Aquatic Research Network, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Roland Jansson
- Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
| | - Helena Machado
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Benoit Marçais
- Université de Lorraine, INRAE, UMR Interactions arbres/microorganismes, F-54000 Nancy, France
| | - Ana C Moreira
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Jonàs Oliva
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain; Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Remigiusz Pielech
- Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Poland
| | - Ana P Rodrigues
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Teresa S David
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal; Instituto Nacional de Investigação Agrária e Veterinária I.P., Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Alejandro Solla
- Faculty of Forestry, Institute for Dehesa Research (INDEHESA), Universidad de Extremadura, Avenida Virgen del Puerto 2, 10600 Plasencia, Spain
| | - Thomas Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic; Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
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11
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Sherwood P, Nordström I, Woodward S, Bohman B, Cleary M. Detecting Pathogenic Phytophthora Species Using Volatile Organic Compounds. Molecules 2024; 29:1749. [PMID: 38675569 PMCID: PMC11052055 DOI: 10.3390/molecules29081749] [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: 01/15/2024] [Revised: 03/30/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
There are several highly damaging Phytophthora species pathogenic to forest trees, many of which have been spread beyond their native range by the international trade of live plants and infested materials. Such introductions can be reduced through the development of better tools capable of the early, rapid, and high-throughput detection of contaminated plants. This study utilized a volatilomics approach (solid-phase microextraction coupled to gas chromatography-mass spectrometry) to differentiate between several Phytophthora species in culture and discriminate between healthy and Phytophthora-inoculated European beech and pedunculate oak trees. We tentatively identified 14 compounds that could differentiate eight Phytophthora species from each other in vitro. All of the Phytophthora species examined, except Phytophthora cambivora, uniquely produced at least one compound not observed in the other species; however, most detected compounds were shared between multiple species. Phytophthora polonica had the most unique compounds and was the least similar of all the species examined. The inoculated seedlings had qualitatively different volatile profiles and could be distinguished from the healthy controls by the presence of isokaurene, anisole, and a mix of three unknown compounds. This study supports the notion that volatiles are suitable for screening plant material, detecting tree pathogens, and differentiating between healthy and diseased material.
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Affiliation(s)
- Patrick Sherwood
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden; (I.N.); (M.C.)
| | - Ida Nordström
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden; (I.N.); (M.C.)
| | - Steve Woodward
- Department of Plant and Soil Science, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, UK;
| | - Björn Bohman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden;
| | - Michelle Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 190, 234 22 Lomma, Sweden; (I.N.); (M.C.)
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12
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Guaschino M, Garello M, Nari L, Zhimo YV, Droby S, Spadaro D. Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease. Front Microbiol 2024; 15:1330865. [PMID: 38577679 PMCID: PMC10991698 DOI: 10.3389/fmicb.2024.1330865] [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: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 04/06/2024] Open
Abstract
Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.
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Affiliation(s)
- Micol Guaschino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | - Marco Garello
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | | | - Yeka V. Zhimo
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Samir Droby
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
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13
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Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy Z, Baharuddin B, Bakonyi J, Broders K, Cacciola S, Chang TT, Chi N, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu CH, Garcia L, Hieno A, Ho HH, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira L, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu P, Tomić Z, Tomšovský M, Uematsu S, Webber J, Zeng HC, Zheng FC, Brasier C, Horta Jung M. Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Stud Mycol 2024; 107:251-388. [PMID: 38600961 PMCID: PMC11003442 DOI: 10.3114/sim.2024.107.04] [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: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 04/12/2024] Open
Abstract
During 25 surveys of global Phytophthora diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of Phytophthora major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels ca. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the Phytophthora clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single Phytophthora clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in Phytophthora. Taxonomic novelties: New species: Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenković, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M. Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora furcata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I. Milenković, Phytophthora indonesiensis T. Jung, M. Tarigan, L. Oliveira & I. Milenković, Phytophthora japonensis T. Jung, A. Hieno, H. Masuya & J.F. Webber, Phytophthora limosa T. Corcobado, T. Majek, M. Ferreira & T. Jung, Phytophthora macroglobulosa H.-C. Zeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenković & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora nimia T. Jung, H. Masuya, A. Hieno & C.M. Brasier, Phytophthora oblonga T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora obovoidea T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora obturata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora penetrans T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora platani T. Jung, A. Pérez-Sierra, S.O. Cacciola & M. Horta Jung, Phytophthora proliferata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora pseudocapensis T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pseudocitrophthora T. Jung, S.O. Cacciola, J. Bakonyi & M. Horta Jung, Phytophthora pseudofrigida T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora pseudoccultans T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pyriformis T. Jung, Y. Balci, K.D. Boders & M. Horta Jung, Phytophthora sumatera T. Jung, M. Tarigan, M. Junaid & A. Durán, Phytophthora transposita T. Jung, K. Kageyama, C.M. Brasier & H. Masuya, Phytophthora vacuola T. Jung, H. Masuya, K. Kageyama & J.F. Webber, Phytophthora valdiviana T. Jung, E. Sanfuentes von Stowasser, A. Durán & M. Horta Jung, Phytophthora variepedicellata T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora vietnamensis T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora ×australasiatica T. Jung, N.M. Chi, M. Tarigan & M. Horta Jung, Phytophthora ×lusitanica T. Jung, M. Horta Jung, C. Maia & I. Milenković, Phytophthora ×taiwanensis T. Jung, T.-T. Chang, H.-S. Fu & M. Horta Jung. Citation: Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy ZÁ, Baharuddin B, Bakonyi J, Broders KD, Cacciola SO, Chang T-T, Chi NM, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu C-H, Garcia L, Hieno A, Ho H-H, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira LSS, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu PQ, Tomić Z, Tomšovský M, Uematsu S, Webber JF, Zeng H-C, Zheng F-C, Brasier CM, Horta Jung M (2024). Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Studies in Mycology 107: 251-388. doi: 10.3114/sim.2024.107.04.
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Affiliation(s)
- T. Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
| | - I. Milenković
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Belgrade, Faculty of Forestry, 11030 Belgrade, Serbia
| | - Y. Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, Maryland, 20737 USA
| | - J. Janoušek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - T. Kudláček
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Greifswald, Institute for Mathematics and Computer Science & Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Z.Á. Nagy
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - B. Baharuddin
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - J. Bakonyi
- HUN-REN Centre for Agricultural Research, Plant Protection Institute, ELKH, 1022 Budapest, Hungary
| | - K.D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, República de Panamá
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA
| | - S.O. Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - T.-T. Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - N.M. Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - T. Corcobado
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Cravador
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, University of Algarve, 8005-130 Faro, Portugal
| | - B. Đorđević
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Durán
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - M. Ferreira
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - C.-H. Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - L. Garcia
- Universidad Nacional Agraria, Carretera Norte, Managua 11065, Nicaragua
| | - A. Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - H.-H. Ho
- Department of Biology, State University of New York, New Paltz, New York 12561, USA
| | - C. Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| | - M. Junaid
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - K. Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - T. Kuswinanti
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - C. Maia
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
| | - T. Májek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - H. Masuya
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687, Japan
| | - G. Magnano di San Lio
- University Mediterranea of Reggio Calabria, Department of Agriculture, 89124 Reggio Calabria, Italy
| | | | - N. Nasri
- The United Graduate School of Agricultural Science, Ehime University, Matsuyama, 790-8566, Japan
| | - L.S.S. Oliveira
- Research and Development, Bracell, Alagoinhas, Bahia 48030-300, Brazil
| | - A. Pane
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - A. Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - A. Rosmana
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - E. Sanfuentes von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de Biotecnología, Universidad de Concepción, 4030000 Concepción, Chile
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39A, 07100 Sassari, Italy
| | - R. Singh
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Z. Stanivuković
- University of Banja Luka, Faculty of Forestry, 78000 Banja Luka, Bosnia and Herzegovina
| | - M. Tarigan
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - P.Q. Thu
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - Z. Tomić
- Center for Plant Protection, Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia
| | - M. Tomšovský
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - S. Uematsu
- Laboratory of Molecular and Cellular Biology, Dept. of Bioregulation and Bio-interaction, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - J.F. Webber
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - H.-C. Zeng
- The Institute of Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - F.-C. Zheng
- College of Environment and Plant Protection, Hainan University, Baodoa Xincun, Danzhou City, Hainan 571737, China
| | - C.M. Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - M. Horta Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
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Dhali R, Dey T, Tewari S, Roy SG. A Survey of Phytophthora spp. in Eastern Indian Nurseries and Their Sensitivity to Six Oomycete-Targeted Commercial Fungicides. PLANT DISEASE 2024; 108:486-501. [PMID: 37498632 DOI: 10.1094/pdis-10-22-2341-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
A survey of the flori-horticultural nurseries in eastern India found Phytophthora nicotianae to be the most widespread Phytophthora species associated with different foliar symptoms of nursery plants and identified the presence of P. palmivora in eastern Indian nurseries for the first time. The survey also led to the first worldwide finding of P. nicotianae on Dipteracanthus prostratus (Poir.) Nees; Ocimum tenuiflorum L. (syn. Ocimum sanctum L.); Philodendron xanadu Croat, Mayo & J. Boos; and Pyrostegia venusta (Ker-Gawl.) Miers and P. palmivora on Episcia cupreata (Hook.) Hanst., as well as the first report from India of P. nicotianae on Spathiphyllum wallisii Regel; Anthurium andraeanum Linden ex André; and Adenium obesum (Forsk.) Roem. & Schult. Sensitivity to commercial fungicides Glazer 35WS, Rallis India (metalaxyl, FRAC code 4); Ridomil Gold, Syngenta (mefenoxam + mancozeb); Revus, Syngenta (mandipropamid, FRAC code 40); Aliette Bayer (fosetyl-Al, FRAC code 33); Acrobat, BASF (dimethomorph, FRAC code 40); and Amistar, Syngenta (azoxystrobin, FRAC code 11) was analyzed, showing EC50 values ranging from 0.75 to 16.39 ppm, 0.74 to 1.45 ppm, 2.43 to 17.21 ppm, 63.81 to 327.31 ppm, 8.88 to 174.69 ppm, and 0.1 to 1.13 ppm, respectively, with no cross-resistance of the isolates to the fungicides. The baseline information produced about these Phytophthora spp. from ornamental and horticultural host associations could help prevent the pathogens from becoming primary drivers of new disease outbreaks and their large-scale distribution beyond their natural endemic ranges.
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Affiliation(s)
- Rikta Dhali
- Department of Botany, West Bengal State University, Barasat, Kolkata 700126, India
| | - Tanmoy Dey
- Department of Botany, West Bengal State University, Barasat, Kolkata 700126, India
| | | | - Sanjoy Guha Roy
- Department of Botany, West Bengal State University, Barasat, Kolkata 700126, India
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15
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Caballol M, Redondo MÁ, Catalán N, Corcobado T, Jung T, Marçais B, Milenković I, Nemesio-Gorriz M, Stenlid J, Oliva J. Climate acts as an environmental filter to plant pathogens. THE ISME JOURNAL 2024; 18:wrae010. [PMID: 38366172 PMCID: PMC10926774 DOI: 10.1093/ismejo/wrae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth, and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.
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Affiliation(s)
- Maria Caballol
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida 25198, Spain
- Joint Research Unit CTFC – AGROTECNIO-CERCA, Lleida 25198, Spain
| | - Miguel Ángel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala 750 07, Sweden
| | - Núria Catalán
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona 08034, Spain
| | - Tamara Corcobado
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Brno 613 00, Czech Republic
- Austrian Research Centre for Forests (BFW), Seckendorff-Gudent-Weg 8, Vienna 1131, Austria
| | - Thomas Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Brno 613 00, Czech Republic
| | - Benoît Marçais
- Université de Lorraine - INRAE, UMR Interactions Arbres/Microorganismes, Nancy 54000, France
| | - Ivan Milenković
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Brno 613 00, Czech Republic
- University of Belgrade-Faculty of Forestry, Belgrade 11030, Serbia
| | | | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala 750 07, Sweden
| | - Jonàs Oliva
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida 25198, Spain
- Joint Research Unit CTFC – AGROTECNIO-CERCA, Lleida 25198, Spain
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16
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Abad Z, Burgess T, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl J, Verkleij G, Broders K, Schena L, Redford A. Phytophthora : taxonomic and phylogenetic revision of the genus. Stud Mycol 2023; 106:259-348. [PMID: 38298569 PMCID: PMC10825748 DOI: 10.3114/sim.2023.106.05] [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: 05/12/2023] [Accepted: 08/19/2023] [Indexed: 02/02/2024] Open
Abstract
Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.
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Affiliation(s)
- Z.G. Abad
- USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory, USA;
| | - T.I. Burgess
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, Perth, WA, Australia;
| | - T. Bourret
- Department of Plant Pathology, University of California, Davis, CA, USA,
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8, 3584 CT Utrecht, Netherlands,
| | - S.O. Cacciola
- Department of Agricultural, Food and Environment, University of Catania, Italy;
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Italy;
| | - R. Mathew
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - B. Kasiborski
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - S. Srivastava
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - K. Kageyama
- River Basin Research Center, Gifu University, Japan,
| | - J.C. Bienapfl
- USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory, USA;
| | - G. Verkleij
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8, 3584 CT Utrecht, Netherlands,
| | - K. Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA;
| | - L. Schena
- Dipartimento di Agraria, Mediterranean University of Reggio Calabria, Italy,
| | - A.J. Redford
- USDA APHIS PPQ S&T Identification Technology Program, USA
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Fletcher K, Michelmore R. Genome-Enabled Insights into Downy Mildew Biology and Evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:165-183. [PMID: 37268005 DOI: 10.1146/annurev-phyto-021622-103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, California, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, California, USA
- Department of Plant Sciences; Department of Molecular and Cellular Biology; Department of Medical Microbiology and Immunology, University of California, Davis, California, USA;
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18
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Fuller E, Germaine KJ, Rathore DS. The Good, the Bad, and the Useable Microbes within the Common Alder ( Alnus glutinosa) Microbiome-Potential Bio-Agents to Combat Alder Dieback. Microorganisms 2023; 11:2187. [PMID: 37764031 PMCID: PMC10535473 DOI: 10.3390/microorganisms11092187] [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: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Common Alder (Alnus glutinosa (L.) Gaertn.) is a tree species native to Ireland and Europe with high economic and ecological importance. The presence of Alder has many benefits including the ability to adapt to multiple climate types, as well as aiding in ecosystem restoration due to its colonization capabilities within disturbed soils. However, Alder is susceptible to infection of the root rot pathogen Phytophthora alni, amongst other pathogens associated with this tree species. P. alni has become an issue within the forestry sector as it continues to spread across Europe, infecting Alder plantations, thus affecting their growth and survival and altering ecosystem dynamics. Beneficial microbiota and biocontrol agents play a crucial role in maintaining the health and resilience of plants. Studies have shown that beneficial microbes promote plant growth as well as aid in the protection against pathogens and abiotic stress. Understanding the interactions between A. glutinosa and its microbiota, both beneficial and pathogenic, is essential for developing integrated management strategies to mitigate the impact of P. alni and maintain the health of Alder trees. This review is focused on collating the relevant literature associated with Alder, current threats to the species, what is known about its microbial composition, and Common Alder-microbe interactions that have been observed worldwide to date. It also summarizes the beneficial fungi, bacteria, and biocontrol agents, underpinning genetic mechanisms and secondary metabolites identified within the forestry sector in relation to the Alder tree species. In addition, biocontrol mechanisms and microbiome-assisted breeding as well as gaps within research that require further attention are discussed.
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Affiliation(s)
- Emma Fuller
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
| | - Kieran J. Germaine
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
| | - Dheeraj Singh Rathore
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
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19
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Wang Z, Su C, Hu W, Su Q, Luan Y. The effectors of Phytophthora infestans impact host immunity upon regulation of antagonistic hormonal activities. PLANTA 2023; 258:59. [PMID: 37530861 DOI: 10.1007/s00425-023-04215-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
MAIN CONCLUSION Phytophthora infestans effectors manipulate the antagonism of host hormones to interfere with the immune response of plants at different infection stages. Phytophthora infestans (P. infestans) poses a serious threat to global crop production, and its effectors play an indispensable role in its pathogenicity. However, the function of these effectors during the switch from biotrophy to necrotrophy of P. infestans remains unclear. Further research on the effectors that manipulate the antagonistic response of host hormones is also lacking. In this study, a coexpression analysis and infection assays were performed to identify distinct gene expression changes in both P. infestans and tomato. During the switch from biotrophy to necrotrophy, P. infestans secretes three types of effectors to interfere with host salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) levels. The three aforementioned effectors also regulate the host gene expression including NPR1, TGA2.1, PDF1.2, NDR1, ERF3, NCED6, GAI4, which are involved in hormone crosstalk. The changes in plant hormones are mediated by the three types of effectors, which may accelerate infection and drive completion of the P. infestans lifecycle. Our findings provide new insight into plant‒pathogen interactions that may contribute to the prevention growth of hemibiotrophic pathogens.
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Affiliation(s)
- Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Wenyun Hu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Qiao Su
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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20
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Corcobado T, Cech TL, Daxer A, Ďatková H, Janoušek J, Patra S, Jahn D, Hüttler C, Milenković I, Tomšovský M, Jung MH, Jung T. Phytophthora, Nothophytophthora and Halophytophthora diversity in rivers, streams and riparian alder ecosystems of Central Europe. Mycol Prog 2023; 22:50. [PMID: 37323627 PMCID: PMC10264269 DOI: 10.1007/s11557-023-01898-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023]
Abstract
Waterways are ideal pathways for Phytophthora dispersal and potential introduction to terrestrial ecosystems. While many Phytophthora species from phylogenetic clades 6, 9 and 10 are predominant oomycetes in watercourses due to their adaptation to a lifestyle as saprotrophs and opportunistic pathogens of riparian plants, species from clades 2, 7 and 8 are predominantly soil- or airborne using aquatic habitats as temporal niches for spreading and invading terrestrial sites along the watercourses. In contrast to forest ecosystems, knowledge of Phytophthora diversity in watercourses in Central Europe is limited. Between 2014 and 2019 extensive surveys of streams and rivers were undertaken across Austria, in South Moravia, Czech Republic and Žilina province, Slovakia to unveil the diversity and distribution of Phytophthora and related oomycetes. In addition, in Austria riparian forests of black alder (Alnus glutinosa) and grey alder (A. incana) in lowlands and in the Alps were examined. A variety of Phytophthora species from clades 2, 6, 7, 8, 9 and 10 were isolated, with clade 6 species showing the widest distribution and abundance. Furthermore, interspecific clade 6 hybrids and other oomycetes such as Halophytophthora fluviatilis and undescribed Nothophytophthora spp. were also obtained. In riparian alders, symptoms of Phytophthora infections were associated with species from the P. × alni complex and P. plurivora. Phytophthora plurivora was most common in alder stands whereas P. uniformis was the oomycete species occurring at the highest altitude in alpine riparian areas. Supplementary Information The online version contains supplementary material available at 10.1007/s11557-023-01898-1.
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Affiliation(s)
- Tamara Corcobado
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Natural Hazards and Landscape, Unit of Phytopathology, Department of Forest Protection, Federal Research and Training Centre for Forests, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Thomas L. Cech
- Natural Hazards and Landscape, Unit of Phytopathology, Department of Forest Protection, Federal Research and Training Centre for Forests, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Andreas Daxer
- Natural Hazards and Landscape, Unit of Phytopathology, Department of Forest Protection, Federal Research and Training Centre for Forests, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Henrieta Ďatková
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Josef Janoušek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Sneha Patra
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Global Change Research Institute of the Czech Academy of Sciences, Belidla 986/4a, 603 00 Brno, Czech Republic
| | - Daniella Jahn
- Natural Hazards and Landscape, Unit of Phytopathology, Department of Forest Protection, Federal Research and Training Centre for Forests, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Christine Hüttler
- Natural Hazards and Landscape, Unit of Phytopathology, Department of Forest Protection, Federal Research and Training Centre for Forests, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Ivan Milenković
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Faculty of Forestry, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia
| | - Michal Tomšovský
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Marília Horta Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Phytophthora Research and Consultancy, Am Rain 9, 83131 Nußdorf, Germany
| | - Thomas Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Phytophthora Research and Consultancy, Am Rain 9, 83131 Nußdorf, Germany
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21
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Raco M, Jung T, Horta Jung M, Chi NM, Botella L, Suzuki N. Sequence and phylogenetic analysis of a novel alphaendornavirus, the first virus described from the oomycete plant pathogen Phytophthora heveae. Arch Virol 2023; 168:158. [PMID: 37166518 PMCID: PMC10175314 DOI: 10.1007/s00705-023-05786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Here, we report the discovery and complete genome sequence of a novel virus, designated as "Phytophthora heveae alphaendornavirus 1" (PhAEV1), from a single isolate of the plant pathogenic oomycete Phytophthora heveae (kingdom Stramenipila) isolated from a tropical evergreen lowland rainforest in northern Vietnam. PhAEV1 was detected by both cellulose affinity chromatography of dsRNA and high-throughput sequencing of total RNA, and its presence and sequence were confirmed by RT-PCR and Sanger sequencing. The PhAEV1 genome, 12,820 nucleotides (nt) in length, was predicted to encode a single large polyprotein with the catalytic core domain of viral (superfamily 1) RNA helicase (HEL, amino acid [aa] positions 1,287-1,531), glycosyltransferase (GT, aa positions ca. 2,800-3,125), and RNA-directed RNA polymerase (RdRp, aa positions 3,875-4,112). PhAEV1 is the most similar to Phytophthora cactorum alphaendornavirus 3, sharing 39.4% and 39.1% nt and aa sequence identity, respectively. In addition to the first 5'-terminal AUG codon, three additional in-frame methionine codons were found in close proximity (nt 14-16, 96-98, and 176-178), suggesting potential additional translation initiation sites. Conserved RdRp motifs (A-E) similar to those detected in related endornaviruses were identified in PhAEV1, as well as in several previously described alphaendornaviruses from other Phytophthora species in which these motifs had not been identified previously. Phylogenetic analysis showed that PhAEV1 clusters with members of the genus Alphaendornavirus in the family Endornaviridae and is basal to two other alphaendornaviruses described from another oomycete, Phytophthora cactorum. PhAEV1 is the first virus reported in P. heveae.
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Grants
- CZ.02.1.01/0.0/0.0/15_003/0000453 European Regional Development Fund, project Phytophthora Research Centre
- LDF_VP_2021047 Specific University Research Fund of the Faculty of Forestry and Wood Technology, Mendel University in Brno
- KAKENHI 21H05035 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 21K18222 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 16H06436 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 16H06429 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 16K21723 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
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Affiliation(s)
- Milica Raco
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00.
| | - Thomas Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00
| | - Marilia Horta Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00
| | - Nguyen Minh Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, 10000, Vietnam
| | - Leticia Botella
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 7100046, Japan, Chuo 2-20-1
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22
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Jung T, Balci Y, Broders KD, Milenković I, Janoušek J, Kudláček T, Đorđević B, Horta Jung M. Synchrospora gen. nov., a New Peronosporaceae Genus with Aerial Lifestyle from a Natural Cloud Forest in Panama. J Fungi (Basel) 2023; 9:517. [PMID: 37233228 PMCID: PMC10218844 DOI: 10.3390/jof9050517] [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: 03/14/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023] Open
Abstract
During a survey of Phytophthora diversity in Panama, fast-growing oomycete isolates were obtained from naturally fallen leaves of an unidentified tree species in a tropical cloud forest. Phylogenetic analyses of sequences from the nuclear ITS, LSU and ßtub loci and the mitochondrial cox1 and cox2 genes revealed that they belong to a new species of a new genus, officially described here as Synchrospora gen. nov., which resided as a basal genus within the Peronosporaceae. The type species S. medusiformis has unique morphological characteristics. The sporangiophores show determinate growth, multifurcating at the end, forming a stunted, candelabra-like apex from which multiple (8 to >100) long, curved pedicels are growing simultaneously in a medusa-like way. The caducous papillate sporangia mature and are shed synchronously. The breeding system is homothallic, hence more inbreeding than outcrossing, with smooth-walled oogonia, plerotic oospores and paragynous antheridia. Optimum and maximum temperatures for growth are 22.5 and 25-27.5 °C, consistent with its natural cloud forest habitat. It is concluded that S. medusiformis as adapted to a lifestyle as a canopy-dwelling leaf pathogen in tropical cloud forests. More oomycete explorations in the canopies of tropical rainforests and cloud forests are needed to elucidate the diversity, host associations and ecological roles of oomycetes and, in particular, S. medusiformis and possibly other Synchrospora taxa in this as yet under-explored habitat.
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Affiliation(s)
- Thomas Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (I.M.); (J.J.); (T.K.); (B.Đ.); (M.H.J.)
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
| | - Yilmaz Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, MD 20737, USA;
| | - Kirk D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, Panama City 0843-03092, Panama;
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604, USA
| | - Ivan Milenković
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (I.M.); (J.J.); (T.K.); (B.Đ.); (M.H.J.)
- Faculty of Forestry, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia
| | - Josef Janoušek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (I.M.); (J.J.); (T.K.); (B.Đ.); (M.H.J.)
| | - Tomáš Kudláček
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (I.M.); (J.J.); (T.K.); (B.Đ.); (M.H.J.)
| | - Biljana Đorđević
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (I.M.); (J.J.); (T.K.); (B.Đ.); (M.H.J.)
| | - Marilia Horta Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (I.M.); (J.J.); (T.K.); (B.Đ.); (M.H.J.)
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
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23
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Santos M, Diánez F, Sánchez-Montesinos B, Huertas V, Moreno-Gavira A, Esteban García B, Garrido-Cárdenas JA, Gea FJ. Biocontrol of Diseases Caused by Phytophthora capsici and P. parasitica in Pepper Plants. J Fungi (Basel) 2023; 9:jof9030360. [PMID: 36983528 PMCID: PMC10051450 DOI: 10.3390/jof9030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
The main objective of this study was to evaluate the ability of Trichoderma aggressivum f. europaeum, T. longibrachiatum, Paecilomyces variotii, and T. saturnisporum as biological control agents (BCAs) against diseases caused by P. capsici and P. parasitica in pepper. For this purpose, their antagonistic activities were evaluated both in vitro and in vivo. We analysed the expression patterns of five defence related genes, CaBGLU, CaRGA1, CaBPR1, CaPTI1, and CaSAR8.2, in leaves. All BCAs showed a high in vitro antagonistic activity, significantly reducing the mycelial growth of P. capsici and P. parasitica. The treatments with T. aggressivum f. europaeum, T. longibrachiatum, and P. variotii substantially reduced the severity of the disease caused by P. capsici by 54, 76, and 70%, respectively, and of the disease caused by P. parasitica by 66, 55, and 64%, respectively. T. saturnisporum had the lowest values of disease reduction. Reinoculation with the four BCAs increased the control of both plant pathogens. Markedly different expression patterns were observed in the genes CaBGLU, CaRGA1, and CaSAR8.2. Based on the results, all four BCAs under study could be used as a biological alternative to chemicals for the control of P. capsici and P. parasitica in pepper with a high success rate.
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Affiliation(s)
- Mila Santos
- Departamento de Agronomía, Escuela Superior de Ingeniería, Universidad de Almería, 04120 Almería, Spain
- Correspondence: ; Tel.: +34-628188339
| | - Fernando Diánez
- Departamento de Agronomía, Escuela Superior de Ingeniería, Universidad de Almería, 04120 Almería, Spain
| | - Brenda Sánchez-Montesinos
- Departamento de Agronomía, División Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Irapuato 36500, Guanajuato, Mexico
| | - Victoria Huertas
- Departamento de Agronomía, Escuela Superior de Ingeniería, Universidad de Almería, 04120 Almería, Spain
| | - Alejandro Moreno-Gavira
- Departamento de Agronomía, Escuela Superior de Ingeniería, Universidad de Almería, 04120 Almería, Spain
| | - Belén Esteban García
- Departamento de Biología y Geología, Edificio CITE IIB, Universidad de Almería, 04120 Almería, Spain
| | - José A. Garrido-Cárdenas
- Departamento de Biología y Geología, Edificio CITE IIB, Universidad de Almería, 04120 Almería, Spain
| | - Francisco J. Gea
- Centro de Investigación, Experimentación y Servicios del Champiñón (CIES), Quintanar del Rey, 16220 Cuenca, Spain
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24
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Tör M, Wood T, Webb A, Göl D, McDowell JM. Recent developments in plant-downy mildew interactions. Semin Cell Dev Biol 2023; 148-149:42-50. [PMID: 36670035 DOI: 10.1016/j.semcdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/20/2023]
Abstract
Downy mildews are obligate oomycete pathogens that attack a wide range of plants and can cause significant economic impacts on commercial crops and ornamental plants. Traditionally, downy mildew disease control relied on an integrated strategies, that incorporate cultural practices, deployment of resistant cultivars, crop rotation, application of contact and systemic pesticides, and biopesticides. Recent advances in genomics provided data that significantly advanced understanding of downy mildew evolution, taxonomy and classification. In addition, downy mildew genomics also revealed that these obligate oomycetes have reduced numbers of virulence factor genes in comparison to hemibiotrophic and necrotrophic oomycetes. However, downy mildews do deploy significant arrays of virulence proteins, including so-called RXLR proteins that promote virulence or are recognized as avirulence factors. Pathogenomics are being applied to downy mildew population studies to determine the genetic diversity within the downy mildew populations and manage disease by selection of appropriate varieties and management strategies. Genome editing technologies have been used to manipulate host disease susceptibility genes in different plants including grapevine and sweet basil and thereby provide new soucres of resistance genes against downy mildews. Previously, it has proved difficult to transform and manipulate downy mildews because of their obligate lifestyle. However, recent exploitation of RNA interference machinery through Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS) indicate that functional genomics in downy mildews is now possible. Altogether, these breakthrough technologies and attendant fundamental understanding will advance our ability to mitigate downy mildew diseases.
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Affiliation(s)
- Mahmut Tör
- Department of Biology, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
| | | | | | - Deniz Göl
- Department of Biology, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - John M McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061-0329, USA
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25
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Coomber A, Saville A, Carbone I, Ristaino JB. An open-access T-BAS phylogeny for emerging Phytophthora species. PLoS One 2023; 18:e0283540. [PMID: 37011062 PMCID: PMC10069789 DOI: 10.1371/journal.pone.0283540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/10/2023] [Indexed: 04/05/2023] Open
Abstract
Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.
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Affiliation(s)
- Allison Coomber
- Department of Entomology and Plant Pathology, NC State University, Raleigh, North Carolina, United States of America
- Functional Genomics Program, NC State University, Raleigh, North Carolina, United States of America
| | - Amanda Saville
- Department of Entomology and Plant Pathology, NC State University, Raleigh, North Carolina, United States of America
| | - Ignazio Carbone
- Department of Entomology and Plant Pathology, NC State University, Raleigh, North Carolina, United States of America
- Center for Integrated Fungal Research, NC State University, Raleigh, North Carolina, United States of America
| | - Jean Beagle Ristaino
- Department of Entomology and Plant Pathology, NC State University, Raleigh, North Carolina, United States of America
- Emerging Plant Disease and Global Food Security Cluster, NC State University, Raleigh, North Carolina, United States of America
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26
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Kronmiller BA, Feau N, Shen D, Tabima JF, Ali SS, Armitage AD, Arredondo F, Bailey BA, Bollmann SR, Dale A, Harrison RJ, Hrywkiw K, Kasuga T, McDougal R, Nellist CF, Panda P, Tripathy S, Williams NM, Ye W, Wang Y, Hamelin RC, Grünwald NJ. Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:26-46. [PMID: 36306437 DOI: 10.1094/mpmi-06-22-0133-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Brent A Kronmiller
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Javier F Tabima
- Department of Biology, Clark University, Worcester, MA, U.S.A
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, U.S.A
| | - Andrew D Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, U.K
| | - Felipe Arredondo
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, U.S.A
| | - Stephanie R Bollmann
- Department of Integrative Biology, Oregon State University, Corvallis, OR, U.S.A
| | - Angela Dale
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
- SC-New Construction Materials, FPInnovations, Vancouver, V6T 1Z4, Canada
| | | | - Kelly Hrywkiw
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, U.S.A
| | - Rebecca McDougal
- Scion (Zealand Forest Research Institute), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua, New Zealand
| | | | - Preeti Panda
- The New Zealand Institute for Plant and Food Research Ltd, 74 Gerald Street, Lincoln, 7608, New Zealand
| | | | - Nari M Williams
- Scion (Zealand Forest Research Institute), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua, New Zealand
- Department of Pathogen Ecology and Control, Plant and Food Research, Private Bag 1401, Havelock North, New Zealand
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département des sciences du bois et de la forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, U.S.A
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27
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Antonelli C, Biscontri M, Tabet D, Vettraino AM. The Never-Ending Presence of Phytophthora Species in Italian Nurseries. Pathogens 2022; 12:15. [PMID: 36678363 PMCID: PMC9863022 DOI: 10.3390/pathogens12010015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Plant trade coupled with climate change has led to the increased spread of well-known and new Phytophthora species, a group of fungus-like organisms placed in the Kingdom Chromista. Their presence in plant nurseries is of particular concern because they are responsible for many plant diseases, with high environmental, economic and social impacts. This paper offers a brief overview of the current status of Phytophthora species in European plant nurseries. Focus was placed on Italian sites. Despite the increasing awareness of the risk of Phytophthora spread and the management strategies applied for controlling it, the complexity of the Phytophthora community in the horticulture industry is increasing over time. Since the survey carried out by Jung et al. (2016), new Phytophthora taxa and Phytophthora-host associations were identified. Phytophthorahydropathica, P. crassamura, P. pseudocryptogea and P. meadii were reported for the first time in European plant nurseries, while P. pistaciae, P. mediterranea and P. heterospora were isolated from Italian ornamental nurseries. Knowledge of Phytophthora diversity in plant nurseries and the potential damage caused by them will help to contribute to the development of early detection methods and sustainable management strategies to control Phytophthora spread in the future.
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Affiliation(s)
| | | | | | - Anna Maria Vettraino
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
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28
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Influence of Culture Media and Environmental Factors (Water Potential and Temperature) on Mycelial Growth of Phytopythium vexans (de Bary), the Causal Agent of Dieback Disease in Apple Trees. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study aimed at evaluating the effects of culture media and environmental factors (temperature and water potential (Ψw)) on the growth of the pathogenic fungus Phytopythium vexans (de Bary) associated with root rot and dieback disease in apple trees. Tomato agar, potato dextrose agar (PDA), and soybean agar were the most favourable for rapid mycelial growth, with optimum growth recorded for PDA medium. To determine the environmental conditions that promoted the development of this phytopathogen, the effects of temperature (5–30 °C), water potential (Ψw) (−15.54; −0.67 MPa) (0.89–0.995 aw), and their interaction were evaluated on the in vitro radial growth rates of the five isolates of P. vexans and on their latency phase (time period prior to growth). The results of this study showed that temperature, water potential, and their interaction had significant effects (p < 0.001) on the radial growth rates and latency phases of all tested P. vexans isolates. All isolates were able to grow throughout the temperature range (5 to 30 °C), with the maximum radial growth rate being observed at the highest temperatures, 25–30 °C. Growth was seen to be faster at −0.67 MPa (0.995 aw) at 25 °C and 30 °C. No growth was observed at Ψw < −5.44 MPa (0.96 aw), regardless of the temperature. It was found that the length of the latency phase depended significantly on both environmental factors. The longest latency phases (5 days on average) were recorded at a temperature of 5 °C and Ψw of −0.67 MPa (0.995 aw) and −2.69 MPa (0.98 aw), while the shortest latency phases were observed at a temperature of 30 °C and a Ψw of −0.67 MPa (0.995 aw), with an average of 0.2 days. The findings from this study could help to understand the impact of these environmental factors on the occurrence of diseases caused by P. vexans and more likely to design a reliable preventive control strategy based on the avoidance of conditions that play in favour of the phytopathogen.
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