1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Burgess TI, White D, Sapsford SJ. Comparison of Primers for the Detection of Phytophthora (and Other Oomycetes) from Environmental Samples. J Fungi (Basel) 2022; 8:980. [PMID: 36135707 PMCID: PMC9502258 DOI: 10.3390/jof8090980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 primer combinations have been designed to amplify oomycetes, or more specifically, Phytophthora species, from environmental samples. We used the Illumina sequencing platform to compare 13 primer combinations on mock communities and environmental samples. The primer combinations tested varied significantly in their ability to amplify Phytophthora species in a mock community and from environmental samples; this was due to either low sensitivity (unable to detect species present in low concentrations) or a lack of specificity (an inability to amplify some species even if they were present in high concentrations). Primers designed for oomycetes underestimated the Phytophthora community compared to Phytophthora-specific primers. We recommend using technical replicates, primer combinations, internal controls, and a phylogenetic approach for assigning a species identity to OTUs or ASVs. Particular care must be taken if sampling substrates where hybrid species could be expected. Overall, the choice of primers should depend upon the hypothesis being tested.
Collapse
Affiliation(s)
- Treena I. Burgess
- Phytophthora Science and Management, Harry Butler Institute, Murdoch 6150, Australia
| | - Diane White
- Phytophthora Science and Management, Harry Butler Institute, Murdoch 6150, Australia
| | - Sarah J. Sapsford
- Phytophthora Science and Management, Harry Butler Institute, Murdoch 6150, Australia
- School of Biological Science, University of Canterbury, Christchurch 8401, New Zealand
| |
Collapse
|
6
|
Chen Q, Bakhshi M, Balci Y, Broders K, Cheewangkoon R, Chen S, Fan X, Gramaje D, Halleen F, Jung MH, Jiang N, Jung T, Májek T, Marincowitz S, Milenković I, Mostert L, Nakashima C, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies C, Suhaizan L, Suzuki H, Tian C, Tomšovský M, Úrbez-Torres J, Wang W, Wingfield B, Wingfield M, Yang Q, Yang X, Zare R, Zhao P, Groenewald J, Cai L, Crous P. Genera of phytopathogenic fungi: GOPHY 4. Stud Mycol 2022; 101:417-564. [PMID: 36059898 PMCID: PMC9365048 DOI: 10.3114/sim.2022.101.06] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. Taxonomic novelties: New genera: Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pteridopassalora C. Nakash. & Crous; New species: Ascochyta flava Qian Chen & L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora vinacea J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen & Gramaje, Celoporthe foliorum H. Suzuki, Marinc. & M.J. Wingf., Cercospora alyssopsidis M. Bakhshi, Zare & Crous, Dendrostoma elaeocarpi C.M. Tian & Q. Yang, Didymella chlamydospora Qian Chen & L. Cai, Didymella gei Qian Chen & L. Cai, Didymella ligulariae Qian Chen & L. Cai, Didymella qilianensis Qian Chen & L. Cai, Didymella uniseptata Qian Chen & L. Cai, Endothia cerciana W. Wang. & S.F. Chen, Leptosphaerulina miscanthi Qian Chen & L. Cai, Nigrospora covidalis M. Raza, Qian Chen & L. Cai, Nigrospora globospora M. Raza, Qian Chen & L. Cai, Nigrospora philosophiae-doctoris M. Raza, Qian Chen & L. Cai, Phytophthora transitoria I. Milenković, T. Májek & T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora variabilis T. Jung, M. Horta Jung & I. Milenković, Pseudocercospora delonicicola C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora farfugii C. Nakash., I. Araki, & Ai Ito, Pseudocercospora hardenbergiae Crous & C. Nakash., Pseudocercospora kenyirana C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora perrottetiae Crous, C. Nakash. & C.Y. Chen, Pseudocercospora platyceriicola C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora xenopunicae Crous & C. Nakash.; New combinations: Heterophaeomoniella pinifoliorum (Hyang B. Lee et al.) L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pseudocercospora pruni-grayanae (Sawada) C. Nakash. & Motohashi., Pseudocercospora togashiana (K. Ito & Tak. Kobay.) C. Nakash. & Tak. Kobay., Pteridopassalora nephrolepidicola (Crous & R.G. Shivas) C. Nakash. & Crous, Pteridopassalora lygodii (Goh & W.H. Hsieh) C. Nakash. & Crous; Typification: Epitypification: Botrytis infestans Mont., Cercospora abeliae Katsuki, Cercospora ceratoniae Pat. & Trab., Cercospora cladrastidis Jacz., Cercospora cryptomeriicola Sawada, Cercospora dalbergiae S.H. Sun, Cercospora ebulicola W. Yamam., Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora ixorana J.M. Yen & Lim, Cercospora liquidambaricola J.M. Yen, Cercospora pancratii Ellis & Everh., Cercospora pini-densiflorae Hori & Nambu, Cercospora profusa Syd. & P. Syd., Cercospora pyracanthae Katsuki, Cercospora horiana Togashi & Katsuki, Cercospora tabernaemontanae Syd. & P. Syd., Cercospora trinidadensis F. Stevens & Solheim, Melampsora laricis-urbanianae Tak. Matsumoto, Melampsora salicis-cupularis Wang, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora angiopteridis Goh & W.H. Hsieh, Pseudocercospora basitruncata Crous, Pseudocercospora boehmeriigena U. Braun, Pseudocercospora coprosmae U. Braun & C.F. Hill, Pseudocercospora cratevicola C. Nakash. & U. Braun, Pseudocercospora cymbidiicola U. Braun & C.F. Hill, Pseudocercospora dodonaeae Boesew., Pseudocercospora euphorbiacearum U. Braun, Pseudocercospora lygodii Goh & W.H. Hsieh, Pseudocercospora metrosideri U. Braun, Pseudocercospora paraexosporioides C. Nakash. & U. Braun, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous, Septogloeum punctatum Wakef.; Neotypification: Cercospora aleuritis I. Miyake; Lectotypification: Cercospora dalbergiae S.H. Sun, Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora profusa Syd. & P. Syd., Melampsora laricis-urbanianae Tak. Matsumoto, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous. Citation: Chen Q, Bakhshi M, Balci Y, Broders KD, Cheewangkoon R, Chen SF, Fan XL, Gramaje D, Halleen F, Horta Jung M, Jiang N, Jung T, Májek T, Marincowitz S, Milenković T, Mostert L, Nakashima C, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies CFJ, Suhaizan L, Suzuki H, Tian CM, Tomšovský M, Úrbez-Torres JR, Wang W, Wingfield BD, Wingfield MJ, Yang Q, Yang X, Zare R, Zhao P, Groenewald JZ, Cai L, Crous PW (2022). Genera of phytopathogenic fungi: GOPHY 4. Studies in Mycology 101: 417-564. doi: 10.3114/sim.2022.101.06.
Collapse
Affiliation(s)
- Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - M. Bakhshi
- Department of Botany, Iranian Research Institute of Plant Protection, P.O. Box 19395-1454, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Y. Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, Maryland, 20737 USA
| | - K.D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, República de Panamá
| | - R. Cheewangkoon
- Entomology and Plant Pathology Department, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand, 50200
| | - S.F. Chen
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), Zhanjiang 524022, Guangdong Province, China
| | - X.L. Fan
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - D. Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV). Consejo Superior de Investigaciones Científicas - Universidad de La Rioja - Gobierno de La Rioja. Ctra. LO-20 Salida 13, 26007 Logroño. Spain
| | - F. Halleen
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenboscvh, 7599, South Africa
| | - M. Horta Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - N. Jiang
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - T. Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - T. Májek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - S. Marincowitz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - I. Milenković
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - C. Nakashima
- Graduate school of Bioresources, Mie University, Kurima-machiya 1577, Tsu, Mie, 514-8507, Japan
| | - I. Nurul Faziha
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - M. Pan
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - M. Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - C.F.J. Spies
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - L. Suhaizan
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - H. Suzuki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - C.M. Tian
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - M. Tomšovský
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - J.R. Úrbez-Torres
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - W. Wang
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), Zhanjiang 524022, Guangdong Province, China
| | - B.D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - M.J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Q. Yang
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - X. Yang
- USDA-ARS, Foreign Disease-Weed Science Research Unit, 1301 Ditto Avenue, Fort Detrick, Maryland, 21702 USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, P.O. Box 117, Oak Ridge, Tennessee, 37831 USA
| | - R. Zare
- Department of Botany, Iranian Research Institute of Plant Protection, P.O. Box 19395-1454, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - P. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
7
|
Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation. IMA Fungus 2021; 12:16. [PMID: 34193315 PMCID: PMC8246709 DOI: 10.1186/s43008-021-00068-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/23/2021] [Indexed: 02/06/2023] Open
Abstract
The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
Collapse
|
8
|
Molnar C, Nikolaeva E, Kim S, Olson T, Bily D, Kim JE, Kang S. Phytophthora Diversity in Pennsylvania Nurseries and Greenhouses Inferred from Clinical Samples Collected over Four Decades. Microorganisms 2020; 8:microorganisms8071056. [PMID: 32708553 PMCID: PMC7409235 DOI: 10.3390/microorganisms8071056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022] Open
Abstract
The increasing movement of exotic pathogens calls for systematic surveillance so that newly introduced pathogens can be recognized and dealt with early. A resource crucial for recognizing such pathogens is knowledge about the spatial and temporal diversity of endemic pathogens. Here, we report an effort to build this resource for Pennsylvania (PA) by characterizing the identity and distribution of Phytophthora species isolated from diverse plant species in PA nurseries and greenhouses. We identified 1137 Phytophthora isolates cultured from clinical samples of >150 plant species submitted to the PA Department of Agriculture for diagnosis from 1975 to 2019 using sequences of one or more loci and morphological characteristics. The three most commonly received plants were Abies, Rhododendron, and Pseudotsuga. Thirty-six Phytophthora species identified represent all clades, except 3 and 10, and included a distinct subgroup of a known species and a prospective new species. Prominent pathogenic species such as P. cactorum, P. cinnamomi, P. nicotianae, P. drechsleri, P. pini, P. plurivora, and P. sp. kelmania have been found consistently since 1975. One isolate cultured from Juniperus horizontalis roots did not correspond to any known species, and several other isolates also show considerable genetic variation from any authentic species or isolate. Some species were isolated from never-before-documented plants, suggesting that their host range is larger than previously thought. This survey only provides a coarse picture of historical patterns of Phytophthora encounters in PA nurseries and greenhouses because the isolation of Phytophthora was not designed for a systematic survey. However, its extensive temporal and plant coverage offers a unique insight into the association of Phytophthora with diverse plants in nurseries and greenhouses.
Collapse
Affiliation(s)
- Cody Molnar
- Department of Plant Pathology & Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA; (C.M.); (J.-E.K.)
| | - Ekaterina Nikolaeva
- Bureau of Plant Industry, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA; (S.K.); (T.O.); (D.B.)
- Correspondence: (E.N.); (S.K.); Tel.: +1-717-705-5857 (E.N.); +1-814-863-3846 (S.K.)
| | - Seonghwan Kim
- Bureau of Plant Industry, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA; (S.K.); (T.O.); (D.B.)
| | - Tracey Olson
- Bureau of Plant Industry, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA; (S.K.); (T.O.); (D.B.)
| | - Devin Bily
- Bureau of Plant Industry, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA; (S.K.); (T.O.); (D.B.)
| | - Jung-Eun Kim
- Department of Plant Pathology & Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA; (C.M.); (J.-E.K.)
| | - Seogchan Kang
- Department of Plant Pathology & Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA; (C.M.); (J.-E.K.)
- Correspondence: (E.N.); (S.K.); Tel.: +1-717-705-5857 (E.N.); +1-814-863-3846 (S.K.)
| |
Collapse
|
9
|
Ratti MF, Farrer RA, Cano LM, Faedda R, Goss EM. Evaluation of High-Resolution Melting for Rapid Differentiation of Phytophthora Hybrids and Their Parental Species. PLANT DISEASE 2019; 103:2295-2304. [PMID: 31355734 DOI: 10.1094/pdis-12-18-2291-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phytophthora species hybrids have been repeatedly reported as causing damaging diseases to cultivated and wild plants. Two known hybrids, P. andina and P. × pelgrandis, are pathogens of Solanaceae and ornamentals, respectively, although the extent of their host ranges are unknown. P. andina emerged from hybridization of P. infestans and an unidentified related species, whereas P. × pelgrandis emerged from P. nicotianae and P. cactorum. Considering that hybrids and parental species can coexist in the same regions and to distinguish them usually requires cloning or whole genome sequencing, we aimed to develop a rapid tool to distinguish them. Specifically, we used high-resolution melting (HRM) assays to differentiate genotypes based on their amplicon melting profiles. We designed primers for P. × pelgrandis and parental species based on available sequences of P. nicotianae and P. cactorum nuclear genes containing polymorphisms between species. For P. andina, heterozygous sites from Illumina short reads were used for the same purpose. We identified multiple amplicons exhibiting differences in melting curves between parental species and hybrids. We propose HRM as a rapid method for differentiation of P. andina and P. × pelgrandis hybrids from parental species that could be employed to advance research on these pathogens.
Collapse
Affiliation(s)
- Maria F Ratti
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 U.S.A
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo, Km 30.5 Vía Perimetral. P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Rhys A Farrer
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Roberto Faedda
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 U.S.A
| |
Collapse
|
10
|
Yang X, Hong C. Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species. Front Microbiol 2018; 9:2334. [PMID: 30337915 PMCID: PMC6178919 DOI: 10.3389/fmicb.2018.02334] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/12/2018] [Indexed: 11/13/2022] Open
Abstract
The genus Phytophthora is agriculturally and ecologically important. As the number of Phytophthora species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named Phytophthora species. These genetic markers were the cytochrome-c oxidase 1 (cox1), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (β-tub), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and tigA gene fusion protein (tigA). As indicated by species distance, cox1 had the highest genus-wide resolution, followed by ITS, tigA, and β-tub. Resolution of these four markers also varied with (sub)clade. β-tub alone could readily identify all species in clade 1, cox1 for clade 2, and tigA for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and β-tub (96%) were easier to amplify than cox1 (75%) and tigA (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown Phytophthora isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.
Collapse
Affiliation(s)
- Xiao Yang
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, United States
| | | |
Collapse
|
11
|
Isolation and Pathogenicity of Phytophthora Species from Poplar Plantations in Serbia. FORESTS 2018. [DOI: 10.3390/f9060330] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
12
|
Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands. Persoonia - Molecular Phylogeny and Evolution of Fungi 2018; 40:182-220. [PMID: 30505001 PMCID: PMC6146643 DOI: 10.3767/persoonia.2018.40.08] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/29/2018] [Indexed: 11/25/2022]
Abstract
Most members of the oomycete genus Phytophthora are primary plant pathogens. Both soil- and airborne Phytophthora species are able to survive adverse environmental conditions with enduring resting structures, mainly sexual oospores, vegetative chlamydospores and hyphal aggregations. Soilborne Phytophthora species infect fine roots and the bark of suberized roots and the collar region with motile biflagellate zoospores released from sporangia during wet soil conditions. Airborne Phytophthora species infect leaves, shoots, fruits and bark of branches and stems with caducous sporangia produced during humid conditions on infected plant tissues and dispersed by rain and wind splash. During the past six decades, the number of previously unknown Phytophthora declines and diebacks of natural and semi-natural forests and woodlands has increased exponentially, and the vast majority of them are driven by introduced invasive Phytophthora species. Nurseries in Europe, North America and Australia show high infestation rates with a wide range of mostly exotic Phytophthora species. Planting of infested nursery stock has proven to be the main pathway of Phytophthora species between and within continents. This review provides insights into the history, distribution, aetiology, symptomatology, dynamics and impact of the most important canker, decline and dieback diseases caused by soil- and airborne Phytophthora species in forests and natural ecosystems of Europe, Australia and the Americas.
Collapse
|
13
|
Bily DS, Diehl SV, Cook M, Wallace LE, Sims LL, Watson C, Baird RE. Temporal and Locational Variations of a Phytophthora spp. Community in an Urban Forested Water Drainage and Stream-Runoff System. SOUTHEAST NAT 2018. [DOI: 10.1656/058.017.0118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Devin S. Bily
- Department of Sustainable Bioproducts, Mississippi State University, Mississippi State, MS 39762
| | - Susan V. Diehl
- Department of Sustainable Bioproducts, Mississippi State University, Mississippi State, MS 39762
| | - Madeline Cook
- Department of Biological Sciences, Mississippi State University Mississippi State, MS 39762
| | - Lisa E. Wallace
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529
| | - Laura L. Sims
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
| | - Clarence Watson
- University of Arkansas Division of Agriculture, Fayetteville, AR 72701
| | - Richard E. Baird
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| |
Collapse
|
14
|
Yang X, Tyler BM, Hong C. An expanded phylogeny for the genus Phytophthora. IMA Fungus 2017; 8:355-384. [PMID: 29242780 PMCID: PMC5729717 DOI: 10.5598/imafungus.2017.08.02.09] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/31/2017] [Indexed: 10/27/2022] Open
Abstract
A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.
Collapse
Affiliation(s)
- Xiao Yang
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| | - Brett M. Tyler
- Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| |
Collapse
|
15
|
Jung T, Jung M, Scanu B, Seress D, Kovács G, Maia C, Pérez-Sierra A, Chang TT, Chandelier A, Heungens K, van Poucke K, Abad-Campos P, Léon M, Cacciola S, Bakonyi J. Six new Phytophthora species from ITS Clade 7a including two sexually functional heterothallic hybrid species detected in natural ecosystems in Taiwan. PERSOONIA 2017; 38:100-135. [PMID: 29151629 PMCID: PMC5645180 DOI: 10.3767/003158517x693615] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/05/2016] [Indexed: 11/25/2022]
Abstract
During a survey of Phytophthora diversity in natural ecosystems in Taiwan six new species were detected. Multigene phylogeny based on the nuclear ITS, ß-tubulin and HSP90 and the mitochondrial cox1 and NADH1 gene sequences demonstrated that they belong to ITS Clade 7a with P. europaea, P. uniformis, P. rubi and P. cambivora being their closest relatives. All six new species differed from each other and from related species by a unique combination of morphological characters, the breeding system, cardinal temperatures and growth rates. Four homothallic species, P. attenuata, P. flexuosa, P. formosa and P. intricata, were isolated from rhizosphere soil of healthy forests of Fagus hayatae, Quercus glandulifera, Q. tarokoensis, Castanopsis carlesii, Chamaecyparis formosensis and Araucaria cunninghamii. Two heterothallic species, P. xheterohybrida and P. xincrassata, were exclusively detected in three forest streams. All P. xincrassata isolates belonged to the A2 mating type while isolates of P. xheterohybrida represented both mating types with oospore abortion rates according to Mendelian ratios (4-33 %). Multiple heterozygous positions in their ITS, ß-tubulin and HSP90 gene sequences indicate that P. xheterohybrida, P. xincrassata and P. cambivora are interspecific hybrids. Consequently, P. cambivora is re-described as P. xcambivora without nomenclatural act. Pathogenicity trials on seedlings of Castanea sativa, Fagus sylvatica and Q. suber indicate that all six new species might pose a potential threat to European forests.
Collapse
Affiliation(s)
- T. Jung
- Laboratory of Molecular Biotechnology and Phytopathology, Center for Mediterranean Bioresources and Food (MeditBio), University of Algarve, Campus de Gambelas, 8005-130 Faro, Portugal
| | - M.H. Jung
- Laboratory of Molecular Biotechnology and Phytopathology, Center for Mediterranean Bioresources and Food (MeditBio), University of Algarve, Campus de Gambelas, 8005-130 Faro, Portugal
| | - B. Scanu
- Dipartimento di Agraria, Sezione di Patologia vegetale ed Entomologia (SPaVE), Universitá degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - D. Seress
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - G.M. Kovács
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - C. Maia
- Laboratory of Molecular Biotechnology and Phytopathology, Center for Mediterranean Bioresources and Food (MeditBio), University of Algarve, Campus de Gambelas, 8005-130 Faro, Portugal
| | - A. Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - T.-T. Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - A. Chandelier
- Life Sciences Department, Walloon Agricultural Research Centre, 5030 Gembloux, Belgium
| | - K. Heungens
- Plant Sciences Research – Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - K. van Poucke
- Plant Sciences Research – Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - P. Abad-Campos
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - M. Léon
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | - S.O. Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - J. Bakonyi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
16
|
Puglisi I, De Patrizio A, Schena L, Jung T, Evoli M, Pane A, Van Hoa N, Van Tri M, Wright S, Ramstedt M, Olsson C, Faedda R, Magnano di San Lio G, Cacciola SO. Two previously unknown Phytophthora species associated with brown rot of Pomelo (Citrus grandis) fruits in Vietnam. PLoS One 2017; 12:e0172085. [PMID: 28208159 PMCID: PMC5313238 DOI: 10.1371/journal.pone.0172085] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 01/31/2017] [Indexed: 11/19/2022] Open
Abstract
Two distinct Phytophthora taxa were found to be associated with brown rot of pomelo (Citrus grandis), a new disease of this ancestral Citrus species, in the Vinh Long province, Mekong River Delta area, southern Vietnam. On the basis of morphological characters and using the ITS1-5.8S-ITS2 region of the rDNA and the cytochrome oxidase subunit 1 (COI) as barcode genes, one of the two taxa was provisionally named as Phytophthora sp. prodigiosa, being closely related to but distinct from P. insolita, a species in Phytophthora Clade 9, while the other one, was closely related to but distinct from the Clade 2 species P. meadii and was informally designated as Phytophthora sp. mekongensis. Isolates of P. sp. prodigiosa and P. sp. mekongensis were also obtained from necrotic fibrous roots of Volkamer lemon (C. volkameriana) rootstocks grafted with 'King' mandarin (Citrus nobilis) and from trees of pomelo, respectively, in other provinces of the Mekong River Delta, indicating a widespread occurrence of both Phytophthora species in this citrus-growing area. Koch's postulates were fulfilled via pathogenicity tests on fruits of various Citrus species, including pomelo, grapefruit (Citrus x paradisi), sweet orange (Citrus x sinensis) and bergamot (Citrus x bergamia) as well as on the rootstock of 2-year-old trees of pomelo and sweet orange on 'Carrizo' citrange (C. sinensis 'Washington Navel' x Poncirus trifoliata). This is the first report of a Phytophthora species from Clade 2 other than P. citricola and P. citrophthora as causal agent of fruit brown rot of Citrus worldwide and the first report of P. insolita complex in Vietnam. Results indicate that likely Vietnam is still an unexplored reservoir of Phytophthora diversity.
Collapse
Affiliation(s)
- Ivana Puglisi
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Feo di Vito, Reggio Calabria, Italy
| | | | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Feo di Vito, Reggio Calabria, Italy
| | - Thomas Jung
- Phytophthora Research Center Mendel University, Zemedelska 1, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, Am Rain 9, Nußdorf, Germany
| | - Maria Evoli
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Antonella Pane
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Nguyen Van Hoa
- Southern Horticultural Research Institute, My Tho, Tien Giang, Vietnam
| | - Mai Van Tri
- Southern Horticultural Research Institute, My Tho, Tien Giang, Vietnam
| | - Sandra Wright
- Department of Electronics, Mathematics and Natural Sciences, University of Gävle, Gävle, Sweden
| | - Mauritz Ramstedt
- Department of Forest Mycology and Plant Pathology, Swedish Agricultural University (SLU), Uppsala, Sweden
| | - Christer Olsson
- Department of Biological and Environmental Sciences, Gothenburg University, Gothenburg, Sweden
| | - Roberto Faedda
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Gaetano Magnano di San Lio
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Feo di Vito, Reggio Calabria, Italy
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| |
Collapse
|
17
|
Stamler RA, Sanogo S, Goldberg NP, Randall JJ. Phytophthora Species in Rivers and Streams of the Southwestern United States. Appl Environ Microbiol 2016; 82:4696-4704. [PMID: 27235435 PMCID: PMC4984303 DOI: 10.1128/aem.01162-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Phytophthora species were isolated from rivers and streams in the southwestern United States by leaf baiting and identified by sequence analysis of internal transcribed spacer (ITS) ribosomal DNA (rDNA). The major waterways examined included the Rio Grande River, Gila River, Colorado River, and San Juan River. The most prevalent species identified in rivers and streams were Phytophthora lacustris and P. riparia, both members of Phytophthora ITS clade 6. P. gonapodyides, P. cinnamomi, and an uncharacterized Phytophthora species in clade 9 were also recovered. In addition, six isolates recovered from the Rio Grande River were shown to be hybrids of P. lacustris × P. riparia Pathogenicity assays using P. riparia and P. lacustris failed to produce any disease symptoms on commonly grown crops in the southwestern United States. Inoculation of Capsicum annuum with P. riparia was shown to inhibit disease symptom development when subsequently challenged with P. capsici, a pathogenic Phytophthora species. IMPORTANCE Many Phytophthora species are significant plant pathogens causing disease on a large variety of crops worldwide. Closer examinations of streams, rivers, and forest soils have also identified numerous Phytophthora species that do not appear to be phytopathogens and likely act as early saprophytes in aquatic and saturated environments. To date, the Phytophthora species composition in rivers and streams of the southwestern United States has not been evaluated. This article details a study to determine the identity and prevalence of Phytophthora species in rivers and streams located in New Mexico, Arizona, Colorado, Utah, and Texas. Isolated species were evaluated for pathogenicity on crop plants and for their potential to act as biological control agents.
Collapse
Affiliation(s)
- Rio A Stamler
- Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, New Mexico, USA
| | - Soumalia Sanogo
- Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, New Mexico, USA
| | - Natalie P Goldberg
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, New Mexico, USA
| | - Jennifer J Randall
- Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, New Mexico, USA
| |
Collapse
|
18
|
Wang J, Presser JW, Goss EM. Nuclear DNA content of the hybrid plant pathogen Phytophthora andina determined by flow cytometry. Mycologia 2016; 108:899-904. [PMID: 27302049 DOI: 10.3852/15-107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 02/17/2016] [Indexed: 11/10/2022]
Abstract
Phytophthora andina is a heterothallic plant pathogen of Andean solanaceous hosts and is an interspecific hybrid of P. infestans and an unknown Phytophthora species. The objective of this study was to estimate the nuclear DNA content of isolates in three clonal lineages of P. andina relative to P. infestans Twelve isolates of P. andina and six isolates of P. infestans were measured for nuclear DNA content by propidium iodide-stained flow cytometry. We found that the DNA content of P. andina was similar but slightly smaller, on average, than that of our sample of P. infestans isolates. This is consistent with P. andina being a homoploid hybrid rather than allopolyploid hybrid. Nuclear DNA content was more variable among a smaller sample of P. infestans isolates, including a putative triploid isolate from Mexico, but small differences in nuclear DNA content were also observed among P. andina isolates. Both species appear to be able to tolerate significant variation in genome size.
Collapse
Affiliation(s)
- Jianan Wang
- Department of Plant Pathology, PO Box 110680, University of Florida, Gainesville, Florida 32611
| | - Jackson W Presser
- School of Natural Resources and Environment and Emerging Pathogens Institute, PO Box 116455, University of Florida, Gainesville, Florida 32611
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogen Institute, PO Box 110680, University of Florida, Gainesville, Florida 32611
| |
Collapse
|
19
|
Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize. Fungal Biol 2016; 120:975-987. [PMID: 27521629 DOI: 10.1016/j.funbio.2016.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/01/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023]
Abstract
During a study on the phylogenetic relationships between species in the Phytophthora cryptogea complex and related species, Phytophthora erythroseptica and Phytophthora sansomeana, 19 hybrid isolates with multiple polymorphisms in the nuclear sequences were observed. Molecular characterization of hybrids was achieved by sequencing three nuclear (internal transcribed spacers, β-tubulin (TUB), heat shock protein 90) and two mitochondrial (cytochrome c oxidase subunit I (coxI), NADH dehydrogenase subunit I (NADH)) gene regions and cloning of the single-copy nuclear gene, TUB. Based on the molecular studies the hybrid isolates belonged to six distinct groups between P. cryptogea, P. erythroseptica, Phytophthora pseudocryptogea, P. sansomeana, and Phytophthora sp. kelmania. In all cases, only a single coxI and NADH allele was detected and nuclear genes were biparentally inherited, suggesting that the hybrids arose from sexual recombination events. Colony morphology, growth rate, cardinal temperatures, breeding system, and morphology of sporangia, oogonia, oospores, and antheridia were also determined. Some morphological differences between the hybrids and the parental species were noted; however, they were not sufficient to reliably distinguish the taxa and DNA markers from nuclear and mitochondrial genes will to be necessary for their identification. The parental species are all important pathogens of agricultural fields that have been transported globally. With the apparent ease of hybridization within this group there is ample opportunity for virulent hybrids to form, perhaps with extended host ranges.
Collapse
|
20
|
Yang X, Balci Y, Brazee NJ, Loyd AL, Hong CX. A unique species in Phytophthora clade 10, Phytophthora intercalaris sp. nov., recovered from stream and irrigation water in the eastern USA. Int J Syst Evol Microbiol 2016; 66:845-855. [PMID: 26620125 PMCID: PMC4772590 DOI: 10.1099/ijsem.0.000800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel species of the genus Phytophthora was recovered during surveys of stream and nursery irrigation water in Maryland, Massachusetts, North Carolina, Virginia and West Virginia in the USA. The novel species is heterothallic, and all examined isolates were A1 mating type. It produced rare ornamented oogonia and amphigynous antheridia when paired with A2 mating type testers of Phytophthora cinnamomi and Phytophthora cryptogea. Sporangia of this novel species were non-papillate and non-caducous. Thin-walled intercalary chlamydospores were abundant in hemp seed agar and carrot agar, while they were produced only rarely in aged cultures grown in clarified V8 juice agar. Phylogenetic analyses based on sequences of the internal transcribed spacer region and the β-tubulin and mitochondrial cytochrome-c oxidase 1 (cox1) genes indicated that the novel species is phylogenetically close to Phytophthora gallica in Phytophthora clade 10. The novel species has morphological and molecular features that are distinct from those of other species in Phytophthora clade 10. It is formally described here as Phytophthora intercalaris sp. nov. Description of this unique clade-10 species is important for understanding the phylogeny and evolution of Phytophthora clade 10.
Collapse
Affiliation(s)
- X. Yang
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, USA
| | - Y. Balci
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - N. J. Brazee
- UMass Extension, Center for Food, Agriculture and the Environment, University of Massachusetts, Amherst, MA, USA
| | - A. L. Loyd
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - C. X. Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, USA
| |
Collapse
|
21
|
Marano A, Jesus A, de Souza J, Jerônimo G, Gonçalves D, Boro M, Rocha S, Pires-Zottarelli C. Ecological roles of saprotrophic Peronosporales (Oomycetes, Straminipila) in natural environments. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.06.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
Burgess TI. Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species. PLoS One 2015; 10:e0134225. [PMID: 26248187 PMCID: PMC4527719 DOI: 10.1371/journal.pone.0134225] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 07/07/2015] [Indexed: 11/29/2022] Open
Abstract
Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones.
Collapse
Affiliation(s)
- Treena I. Burgess
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- * E-mail:
| |
Collapse
|