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Iglesias D, Stevens K, Sharma A, Diaz-Lara A. A Novel Cryptic Virus Isolated from Galphimia spp. in Mexico. Pathogens 2024; 13:504. [PMID: 38921801 PMCID: PMC11207071 DOI: 10.3390/pathogens13060504] [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: 04/26/2024] [Revised: 06/04/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024] Open
Abstract
Galphimia spp. is a plant employed in traditional medicine in Mexico because of its anxiolytic and sedative effects. Viruses have been associated with different alterations in plants, although asymptomatic agents (i.e., cryptic viruses) are also known. High-throughput sequencing (HTS) allows for the detection of pathogenic and non-pathogenic viral agents in plants, including potential novel viruses. The aim of this study was to investigate the presence of viral agents in two populations of Galphimia spp. by HTS. Sequencing was conducted on an Illumina NextSeq 550 platform, and a putative novel virus was identified. Two contigs showed homology to partitiviruses, and these encoded the RNA-dependent RNA polymerase and coat protein. These proteins showed the highest identities with orthologs in the recently discovered Vitis cryptic virus. A phylogenetic analysis of both RNAs showed that the new virus clusters into the monophyletic genus Deltapartitivirus along with other plant-infecting viruses. The result of the HTS analysis was validated by conventional RT-PCR and Sanger sequencing. A novel virus was discovered in a symptomless Galphimia spp. plant and tentatively named the Galphimia cryptic virus (GCV). This is the first virus discovered in medicinal plants in Mexico.
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Affiliation(s)
- Dianella Iglesias
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA;
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
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2
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Nwe LL, Casonato S, Jones EE. Endophytic fungal isolates from apple tissue: Latent pathogens lurking within? Fungal Biol 2024; 128:1836-1846. [PMID: 38876536 DOI: 10.1016/j.funbio.2024.05.003] [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: 03/30/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/16/2024]
Abstract
Fungal endophytes inhabit a similar ecological niche to that occupied by many phytopathogens, with several pathogens isolated from healthy tissues in their latent phase. This study aimed to evaluate the pathogenicity, the colonisation ability, and the enzyme activity of 37 endophytic fungal isolates recovered from apparently healthy apple shoot and leaf tissues. The pathogenicity of the isolates was assessed on 'Royal Gala' and 'Braeburn' fruit and detached 'Royal Gala' shoots. For the non-pathogenic isolates, their ability to endophytically colonise detached 'Royal Gala' shoots was evaluated. Enzyme activity assays were undertaken to determine whether the pathogenicity of the endophytes was related to the production of the extracellular enzymes, amylase, cellulase, pectinase, protease, and xylanase. Of the 37 isolates studied, eight isolates, representing the genera Colletotrichum, Diaporthe, Fusarium, and Penicillium, were shown to be pathogenic on both apple shoots and fruit. Two isolates identified as Trichoderma atroviride, were pathogenic only on shoots, and three isolates, representing the genus Diaporthe, were pathogenic only on fruit. Of the remaining 24 isolates, 22 (Biscogniauxia (n = 8), Chaetomium (n = 4), Trichoderma (n = 3), Epicoccum (n = 2), Neosetophoma (n = 2), Xylaria (n = 1), Daldinia (n = 1), and Paraphaeosphaeria (n = 1)) were recovered from the inoculated apple shoots but two failed to colonise the shoot tissues. Of the isolates tested, 20 produced amylase, 15 cellulase, 25 pectinase, 26 protease, and 13 xylanase. There was no correlation between the range and type of enzymes produced by the isolates and their pathogenicity or ability to endophytically colonise the shoot tissue. The study showed that approximately one-third (13/37) of the isolates recovered from the apparently healthy apple shoot tissues were observed as latent pathogens. The isolates that did not cause disease symptoms may have the ability to reduce colonisation of apple tissues by pathogens including Neonectria ditissima associated with European canker of apple.
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Affiliation(s)
- Lay Lay Nwe
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, Canterbury, New Zealand
| | - Seona Casonato
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, Canterbury, New Zealand
| | - E Eirian Jones
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, Canterbury, New Zealand.
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Patel J, Allen TW, Buckley B, Chen P, Clubb M, Mozzoni LA, Orazaly M, Florez L, Moseley D, Rupe JC, Shrestha BK, Price PP, Ward BM, Koebernick J. Deciphering genetic factors contributing to enhanced resistance against Cercospora leaf blight in soybean ( Glycine max L.) using GWAS analysis. Front Genet 2024; 15:1377223. [PMID: 38798696 PMCID: PMC11116733 DOI: 10.3389/fgene.2024.1377223] [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: 01/27/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Cercospora leaf blight (CLB), caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is a significant soybean [Glycine max (L.) Merr.] disease in regions with hot and humid conditions causing yield loss in the United States and Canada. There is limited information regarding resistant soybean cultivars, and there have been marginal efforts to identify the genomic regions underlying resistance to CLB. A Genome-Wide Association Study was conducted using a diverse panel of 460 soybean accessions from maturity groups III to VII to identify the genomic regions associated to the CLB disease. These accessions were evaluated for CLB in different regions of the southeastern United States over 3 years. In total, the study identified 99 Single Nucleotide Polymorphism (SNPs) associated with the disease severity and 85 SNPs associated with disease incidence. Across multiple environments, 47 disease severity SNPs and 23 incidence SNPs were common. Candidate genes within 10 kb of these SNPs were involved in biotic and abiotic stress pathways. This information will contribute to the development of resistant soybean germplasm. Further research is warranted to study the effect of pyramiding desirable genomic regions and investigate the role of identified genes in soybean CLB resistance.
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Affiliation(s)
- Jinesh Patel
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Tom W. Allen
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS, United States
| | - Blair Buckley
- LSU AgCenter, Red River Research Station, Bossier City, LA, United States
| | - Pengyin Chen
- Fisher Delta Research Center, MO University of Missouri, Portageville, MO, United States
| | - Michael Clubb
- Fisher Delta Research Center, MO University of Missouri, Portageville, MO, United States
| | - Leandro A. Mozzoni
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - Moldir Orazaly
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - Liliana Florez
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - David Moseley
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - John C. Rupe
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Bishnu K. Shrestha
- LSU AgCenter, Macon Ridge Research Station, Winnsboro, LA, United States
| | - Paul P. Price
- LSU AgCenter, Macon Ridge Research Station, Winnsboro, LA, United States
| | - Brian M. Ward
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA, United States
| | - Jenny Koebernick
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
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Matušinsky P, Florová V, Sedláková B, Mlčoch P, Bleša D. Colonization dynamic and distribution of the endophytic fungus Microdochium bolleyi in plants measured by qPCR. PLoS One 2024; 19:e0297633. [PMID: 38271444 PMCID: PMC10810448 DOI: 10.1371/journal.pone.0297633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Microdochium bolleyi is a fungal endophyte of cereals and grasses proposed as an ideal model organism for studying plant-endophyte interactions. A qPCR-based diagnostic assay was developed to detect M. bolleyi in wheat and Brachypodium distachyon tissues using the species-specific primers MbqITS derived from the ITS of the ribosomal gene. Specificity was tested against 20 fungal organisms associated with barley and wheat. Colonization dynamics, endophyte distribution in the plant, and potential of the seed transmission were analyzed in the wheat and model plant B. distachyon. The colonization of plants by endophyte starts from the germinating seed, where the seed coats are first strongly colonized, then the endophyte spreads to the adjacent parts, crown, roots near the crown, and basal parts of the stem. While in the lower distal parts of roots, the concentration of M. bolleyi DNA did not change significantly in successive samplings (30, 60, 90, 120, and 150 days after inoculation), there was a significant increase over time in the roots 1 cm under crown, crowns and stem bases. The endophyte reaches the higher parts of the base (2-4 cm above the crown) 90 days after sowing in wheat and 150 days in B. distachyon. The endophyte does not reach both host species' leaves, peduncles, and ears. Regarding the potential for seed transmission, endophyte was not detected in harvested grains of plants with heavily colonized roots. Plants grown from seeds derived from parental plants heavily colonized by endophyte did not exhibit any presence of the endophyte, so transmission by seeds was not confirmed. The course of colonization dynamics and distribution in the plant was similar for both hosts tested, with two differences: the base of the wheat stem was colonized earlier, but B. distachyon was occupied more intensively and abundantly than wheat. Thus, the designed species-specific primers could detect and quantify the endophyte in planta.
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Affiliation(s)
- Pavel Matušinsky
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
- Department of Plant Pathology, Agrotest Fyto, Ltd, Kroměříž, Czech Republic
| | - Vendula Florová
- Department of Plant Pathology, Agrotest Fyto, Ltd, Kroměříž, Czech Republic
| | - Božena Sedláková
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Patrik Mlčoch
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Dominik Bleša
- Department of Plant Pathology, Agrotest Fyto, Ltd, Kroměříž, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Del Grosso C, Palmieri D, Marchese L, Melissano L, Lima G. First Report of Diplodia quercivora and Neofusicoccum vitifusiforme Associated with Cankers and Necrosis of Holm Oak ( Quercus ilex) in Declining Stands in Southern Italy. J Fungi (Basel) 2024; 10:35. [PMID: 38248945 PMCID: PMC10820903 DOI: 10.3390/jof10010035] [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: 11/12/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
The emergence of new plant diseases is an increasingly important concern. Climate change is likely to be among the factors causing most of the emerging diseases endangering forest and tree heritage around the world. Such diseases may be caused by latent pathogens or microorganisms cryptically associated with plants. The shift from a non-pathogenic to a pathogenic stage may depend on physiological alterations of the host, environmental changes, and/or stress factors. In some woods of the Salento Peninsula (Apulia Region, Italy), sudden declines of holm oak plants (Quercus ilex L.) have been observed since 2016. The morphological and molecular characterization of representative fungal isolates associated with cankers and necrosis in declining plants indicated that these isolates belong to the Botryosphaeriaceae family, and the most frequent species were Diplodia corticola and Diplodia quercivora, followed by Neofusicoccum vitifusiforme. In artificially inoculated young holm oak plants, both D. corticola and D. quercivora species produced intense and severe subcortical and leaf margin necrosis. N. vitifusiforme, although less aggressive, induced the same symptoms. Our research, in addition to confirming the involvement of D. corticola in olm oak decline, represents the first report of D. quercivora as a new pathogen of Q. ilex in Italy. Furthermore, to the best of our knowledge, we also found N. vitifusiforme as a new pathogen of Q. ilex.
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Affiliation(s)
- Carmine Del Grosso
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
- Institute for Sustainable Plant Protection, National Research Council (CNR), 70126 Bari, Italy
| | - Davide Palmieri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
| | - Lucia Marchese
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
| | - Luigi Melissano
- Department of Agriculture, Environment and Rural Development, Sustainable Management and Protection of Natural and Forest Resources, Apulia Region, 70100 Bari, Italy;
| | - Giuseppe Lima
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
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Chen YJ, Chen HJ, Chung WH. Endophytic Fungal Diversity in Cirsium kawakamii from Taiwan. J Fungi (Basel) 2023; 9:1076. [PMID: 37998881 PMCID: PMC10671896 DOI: 10.3390/jof9111076] [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: 08/21/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
The endophytic fungal diversity of Cirsium kawakamii, a herb indigenous to Taiwan, was analyzed in this study. In addition, some fungal isolates were evaluated for the risk they pose as plant pathogens. In total, 1836 endophytic fungi were isolated from C. kawakamii from Hehuanjian, Puli Township, and Tatachia. They were classified into 2 phyla, 8 classes, 40 families, and 68 genera. Colletotrichum, Fusarium, Phomopsis, and Xylaria, (Ascomycota, Sordariomycetes) were the dominant genera. The genus accumulation curve (based on the bootstrap estimator) was non-asymptotic, with estimated richness significantly exceeding the richness captured by our sampling to date. Considering the collection time, the data indicated significant differences in the proportions of the C. kawakamii endophyte genus from Hehuanjan, Puli Township (across two seasons), and Tatachia. The Shannon and Gini-Simpson indices revealed variations in diversity, with C. kawakamii endophytes (Puli Township in winter) significantly reducing alpha diversity compared with other seasons and locations. Meanwhile, the Gini-Simpson index suggested that there were no significant differences in richness among the four sampling sites. The PCA results unveiled distinct community structures across different locations and seasons, explaining 46.73% of the total variation in fungal community composition significantly affected diversity and richness. In addition, a considerable number of Fusarium isolates exhibited harmful properties towards wheat, potatoes, and apples. It is postulated that these fungi belong to the Fusarium tricinctum species complex (FTSC).
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Affiliation(s)
- Yi-Jeng Chen
- Department of Plant Medicine, National Chiayi University, Chiayi 600, Taiwan;
| | - Hui-Juan Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
- Master Program in Plant Medicine and Good Agricultural Practice, National Chung Hsing University, Taichung 402, Taiwan
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Tsers I, Parfirova O, Moruzhenkova V, Petrova O, Gogoleva N, Vorob’ev V, Gogolev Y, Gorshkov V. A Switch from Latent to Typical Infection during Pectobacterium atrosepticum-Tobacco Interactions: Predicted and True Molecular Players. Int J Mol Sci 2023; 24:13283. [PMID: 37686094 PMCID: PMC10487725 DOI: 10.3390/ijms241713283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both fundamental science and disease management. No studies to date have compared, at the systemic molecular level, the physiological portraits of plants when different infection types (typical and latent) are developed. The only phytopathogenic bacterium for which latent infections were not only widely described but also at least fluently characterized at the molecular level is Pectobacterium atrosepticum (Pba). The present study aimed at the comparison of plant transcriptome responses during typical and latent infections caused by Pba in order to identify and then experimentally verify the key molecular players that act as switchers, turning peaceful plant-Pba coexistence into a typical infection. Based on RNA-Seq, we predicted plant cell wall-, secondary metabolism-, and phytohormone-related genes whose products contributed to the development of the disease or provided asymptomatic plant-Pba interactions. By treatment tests, we confirmed that a switch from latent to typical Pba-caused infection is determined by the plant susceptible responses mediated by the joint action of ethylene and jasmonates.
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Affiliation(s)
- Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Varvara Moruzhenkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Vladimir Vorob’ev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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Anthracnose Controlled by Essential Oils: Are Nanoemulsion-Based Films and Coatings a Viable and Efficient Technology for Tropical Fruit Preservation? Foods 2023; 12:foods12020279. [PMID: 36673370 PMCID: PMC9857729 DOI: 10.3390/foods12020279] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Post-harvest diseases can be a huge problem for the tropical fruit sector. These fruits are generally consumed in natura; thus, their integrity and appearance directly affect commercialization and consumer desire. Anthracnose is caused by fungi of the genus Colletotrichum and affects tropical fruits, resulting in lesions that impair their appearance and consumption. Antifungals generally used to treat anthracnose can be harmful to human health, as well as to the environment. Therefore, essential oils (EO) have been investigated as natural biofungicides, successfully controlling anthracnose symptoms. The hydrophobicity, high volatility, and oxidative instability of essential oils limit their direct application; hence, these oils must be stabilized before food application. Distinct delivery systems have already been proposed to protect/stabilize EOs, and nanotechnology has recently reshaped the food application limits of EOs. This review presents robust data regarding nanotechnology application and EO antifungal properties, providing new perspectives to further improve the results already achieved in the treatment of anthracnose. Additionally, it evaluates the current scenario involving the application of EO directly or incorporated in films and coatings for anthracnose treatment in tropical fruits, which is of great importance, especially for those fruits intended for exportation that may have a prolonged shelf life.
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Abrahão A, Marhan S, Boeddinghaus RS, Nawaz A, Wubet T, Hölzel N, Klaus VH, Kleinebecker T, Freitag M, Hamer U, Oliveira RS, Lambers H, Kandeler E. Microbial drivers of plant richness and productivity in a grassland restoration experiment along a gradient of land-use intensity. THE NEW PHYTOLOGIST 2022; 236:1936-1950. [PMID: 36128644 DOI: 10.1111/nph.18503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Plant-soil feedbacks (PSFs) underlying grassland plant richness and productivity are typically coupled with nutrient availability; however, we lack understanding of how restoration measures to increase plant diversity might affect PSFs. We examined the roles of sward disturbance, seed addition and land-use intensity (LUI) on PSFs. We conducted a disturbance and seed addition experiment in 10 grasslands along a LUI gradient and characterized plant biomass and richness, soil microbial biomass, community composition and enzyme activities. Greater plant biomass at high LUI was related to a decrease in the fungal to bacterial ratios, indicating highly productive grasslands to be dominated by bacteria. Lower enzyme activity per microbial biomass at high plant species richness indicated a slower carbon (C) cycling. The relative abundance of fungal saprotrophs decreased, while pathogens increased with LUI and disturbance. Both fungal guilds were negatively associated with plant richness, indicating the mechanisms underlying PSFs depended on LUI. We show that LUI and disturbance affect fungal functional composition, which may feedback on plant species richness by impeding the establishment of pathogen-sensitive species. Therefore, we highlight the need to integrate LUI including its effects on PSFs when planning for practices that aim to optimize plant diversity and productivity.
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Affiliation(s)
- Anna Abrahão
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
- Department of Biology, Science Center, Federal University of Ceará - UFC, Fortaleza, CE, 60440-900, Brazil
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
| | - Runa S Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
- Landwirtschaftliches Technologiezentrum Augustenberg, 76227, Karlsruhe, Germany
| | - Ali Nawaz
- Department of Community Ecology, UFZ - Helmholtz Center for Environmental Research, 06120, Halle (Saale), Germany
- Department of Civil, Geo and Environmental Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ - Helmholtz Center for Environmental Research, 06120, Halle (Saale), Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, D-48149, Münster, Germany
| | - Valentin H Klaus
- Institute of Agricultural Sciences, ETH Zürich, Universitätstr. 2, 8092, Zürich, Switzerland
| | - Till Kleinebecker
- Institute of Landscape Ecology and Resources Management, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
- Center for International Development and Environmental Research (ZEU), Justus Liebig University Giessen, Senckenbergstrasse 3, 35390, Giessen, Germany
| | - Martin Freitag
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, D-48149, Münster, Germany
| | - Ute Hamer
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, D-48149, Münster, Germany
| | - Rafael S Oliveira
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 13083-970, Campinas, Brazil
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
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Nganga EM, Kyallo M, Orwa P, Rotich F, Gichuhi E, Kimani JM, Mwongera D, Waweru B, Sikuku P, Musyimi DM, Mutiga SK, Ziyomo C, Murori R, Wasilwa L, Correll JC, Talbot NJ. Foliar Diseases and the Associated Fungi in Rice Cultivated in Kenya. PLANTS 2022; 11:plants11091264. [PMID: 35567265 PMCID: PMC9105481 DOI: 10.3390/plants11091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae, in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.
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Affiliation(s)
- Everlyne M. Nganga
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - Martina Kyallo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Philemon Orwa
- Department of Water and Agricultural Resource Management, School of Agriculture, University of Embu, Embu P.O. Box 6-60100, Kenya; (P.O.); (F.R.)
| | - Felix Rotich
- Department of Water and Agricultural Resource Management, School of Agriculture, University of Embu, Embu P.O. Box 6-60100, Kenya; (P.O.); (F.R.)
| | - Emily Gichuhi
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - John M. Kimani
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - David Mwongera
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - Bernice Waweru
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Phoebe Sikuku
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - David M. Musyimi
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - Samuel K. Mutiga
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
- Eastern and Southern Region Office, International Rice Research Institute, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya;
- Correspondence:
| | - Cathrine Ziyomo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Rosemary Murori
- Department of Entomology and Plant Pathology, Division of Agriculture, The University of Arkansas System, Fayetteville, AR 72701, USA;
| | - Lusike Wasilwa
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - James C. Correll
- Eastern and Southern Region Office, International Rice Research Institute, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya;
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, Norwich NR4 7UH, UK;
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12
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Carvalhais LC, Dennis PG, Poudel A, Birt HWG, Bhuiyan SA, Card SD, Joyce PA. Simple solution to preserve plant samples for microbiome analyses. Mol Ecol Resour 2021; 22:1055-1064. [PMID: 34695303 DOI: 10.1111/1755-0998.13538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022]
Abstract
Culture-independent survey techniques are fundamental tools when assessing plant microbiomes. These methods rely on DNA that is carefully preserved after collecting samples to achieve meaningful results. Immediately freezing samples to -80°C after collection is considered one of the most robust methods for preserving samples before DNA extraction but is often impractical. Preservation solutions can solve this problem, but commercially available products are expensive, and there is limited data comparing their efficacy with other preservation methods. In this study, we compared the impact of three methods of sample preservation on plant microbiome surveys: (1) RNAlater, a proprietary preservative, (2) a home-made salt-saturated dimethyl sulphoxide preservation solution (DESS), and (3) freezing at -80°C. DESS-preserved samples, stored at room temperature for up to four weeks, did not show any significant differences to samples frozen at -80°C, while RNAlater inflated bacterial alpha diversity. Preservation treatments did not distinctively influence fungal alpha diversity. Our results demonstrate that DESS is a versatile and inexpensive preservative of DNA in plant material for diversity analyses of fungi and bacteria.
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Affiliation(s)
- Lilia C Carvalhais
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia.,Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Brisbane, Qld, Australia.,School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Amrit Poudel
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia
| | - Henry W G Birt
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Shamsul A Bhuiyan
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia.,Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Brisbane, Qld, Australia
| | - Stuart D Card
- Resilient Agriculture, AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Priya A Joyce
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia.,The University of Queensland, Brisbane, Qld, Australia
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Lundberg DS, Pramoj Na Ayutthaya P, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D. Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 2021; 10:e66186. [PMID: 34292157 PMCID: PMC8387020 DOI: 10.7554/elife.66186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
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Affiliation(s)
- Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | | | - Annett Strauß
- Department of Evolutionary Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Wen-Sui Lo
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Thomas Lahaye
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
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14
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Berestetskiy A, Hu Q. The Chemical Ecology Approach to Reveal Fungal Metabolites for Arthropod Pest Management. Microorganisms 2021; 9:1379. [PMID: 34202923 PMCID: PMC8307166 DOI: 10.3390/microorganisms9071379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Biorational insecticides (for instance, avermectins, spinosins, azadirachtin, and afidopyropen) of natural origin are increasingly being used in agriculture. The review considers the chemical ecology approach for the search for new compounds with insecticidal properties (entomotoxic, antifeedant, and hormonal) produced by fungi of various ecological groups (entomopathogens, soil saprotrophs, endophytes, phytopathogens, and mushrooms). The literature survey revealed that insecticidal metabolites of entomopathogenic fungi have not been sufficiently studied, and most of the well-characterized compounds show moderate insecticidal activity. The greatest number of substances with insecticidal properties was found to be produced by soil fungi, mainly from the genera Aspergillus and Penicillium. Metabolites with insecticidal and antifeedant properties were also found in endophytic and phytopathogenic fungi. It was noted that insect pests of stored products are mostly low sensitive to mycotoxins. Mushrooms were found to be promising producers of antifeedant compounds as well as insecticidal proteins. The expansion of the number of substances with insecticidal properties detected in prospective fungal species is possible by mining fungal genomes for secondary metabolite gene clusters and secreted proteins with their subsequent activation by various methods. The efficacy of these studies can be increased with high-throughput techniques of extraction of fungal metabolites and their analysis by various methods of chromatography and mass spectrometry.
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Affiliation(s)
| | - Qiongbo Hu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China;
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15
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Montoya MRA, Massa GA, Colabelli MN, Ridao ADC. Efficient Agrobacterium tumefaciens-mediated transformation system of Diaporthe caulivora. J Microbiol Methods 2021; 184:106197. [PMID: 33713724 DOI: 10.1016/j.mimet.2021.106197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 11/29/2022]
Abstract
This is the first report describing the genetic transformation of Diaporthe caulivora, the soybean stem canker fungus. A simple and 100% efficient protocol of Agrobacterium tumefaciens-mediated transformation used mycelium as starting material and the hygromycin B resistance and green fluorescent protein (GFP) as a selection and reporter agents, respectively. All transgenic isolates were mitotically stable in two independent experiments and polymerase chain reaction with hygromycin B resistance primers confirmed successful T-DNA integration into the fungal genome. Plant-fungus interaction studies, including pathogenicity, latency, and endophytism, as well as further studies of random and targeted mutagenesis will be possible with GFP-expressing isolates of D. caulivora and other species in the Diaporthe / Phomopsis complex.
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Affiliation(s)
- Marina R A Montoya
- Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible (IPADS Balcarce), INTA - CONICET, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina..
| | - Gabriela A Massa
- Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible (IPADS Balcarce), INTA - CONICET, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina.; Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (FCA, UNMdP), Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - Mabel N Colabelli
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (FCA, UNMdP), Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - Azucena Del Carmen Ridao
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (FCA, UNMdP), Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
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Bautista-Jalón LS, Frenkel O, Tsror Lahkim L, Malcolm GM, Gugino BK, Lebiush S, Hazanovsky M, Milgroom MG, Del Mar Jiménez-Gasco M. Genetic Differentiation of Verticillium dahliae Populations Recovered from Symptomatic and Asymptomatic Hosts. PHYTOPATHOLOGY 2021; 111:149-159. [PMID: 33079020 DOI: 10.1094/phyto-06-20-0230-fi] [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: 06/11/2023]
Abstract
Verticillium dahliae is a soilborne fungal pathogen affecting many economically important crops that can also infect weeds and rotational crops with no apparent disease symptoms. The main research goal was to test the hypothesis that V. dahliae populations recovered from asymptomatic rotational crops and weed species are evolutionarily and genetically distinct from symptomatic hosts. We collected V. dahliae isolates from symptomatic and asymptomatic hosts growing in fields with histories of Verticillium wilt of potato in Israel and Pennsylvania (United States), and used genotyping-by-sequencing to analyze the evolutionary history and genetic differentiation between populations of different hosts. A phylogeny inferred from 26,934 single-nucleotide polymorphisms (SNPs) in 126 V. dahliae isolates displayed a highly clonal structure correlated with vegetative compatibility groups, and isolates grouped in lineages 2A, 2B824, 4A, and 4B, with 77% of the isolates in lineage 4B. The lineages identified in this study were differentiated by host of origin; we found 2A, 2B824, and 4A only in symptomatic hosts but isolates from asymptomatic hosts (weeds, oat, and sorghum) grouped exclusively within lineage 4B, and were genetically indistinguishable from 4B isolates sampled from symptomatic hosts (potato, eggplant, and avocado). Using coalescent analysis of 158 SNPs of lineage 4B, we inferred a genealogy with clades that correlated with geographic origin. In contrast, isolates from asymptomatic and symptomatic hosts shared some of the same haplotypes and were not differentiated. We conclude that asymptomatic weeds and rotational hosts may be potential reservoirs for V. dahliae populations of lineage 4B, which are pathogenic to many cultivated hosts.
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Affiliation(s)
- Laura S Bautista-Jalón
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Volcani Center, Rishon Lezion 7528809, Israel
| | - Leah Tsror Lahkim
- Department of Plant Pathology and Weed Research, Gilat Center, M.P. Negev, 8531100, Israel
| | - Glenna M Malcolm
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Beth K Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Sara Lebiush
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Marina Hazanovsky
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Michael G Milgroom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | - María Del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
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Panstruga R, Moscou MJ. What is the Molecular Basis of Nonhost Resistance? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1253-1264. [PMID: 32808862 DOI: 10.1094/mpmi-06-20-0161-cr] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term "nonhost genes" is misleading and should be avoided. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view of plant immunity.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringer Weg 1, 52056 Aachen, Germany
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, United Kingdom
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18
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Towards consensus on the transfer of Fusarium oxysporum V5w2-enhanced tissue culture banana technology to farmers through public-private partnerships in East Africa. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Halliday FW, Heckman RW, Wilfahrt PA, Mitchell CE. Eutrophication, biodiversity loss, and species invasions modify the relationship between host and parasite richness during host community assembly. GLOBAL CHANGE BIOLOGY 2020; 26:4854-4867. [PMID: 32427383 DOI: 10.1111/gcb.15165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/02/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Host and parasite richness are generally positively correlated, but the stability of this relationship in response to global change remains poorly understood. Rapidly changing biotic and abiotic conditions can alter host community assembly, which in turn, can alter parasite transmission. Consequently, if the relationship between host and parasite richness is sensitive to parasite transmission, then changes in host composition under various global change scenarios could strengthen or weaken the relationship between host and parasite richness. To test the hypothesis that host community assembly can alter the relationship between host and parasite richness in response to global change, we experimentally crossed host diversity (biodiversity loss) and resource supply to hosts (eutrophication), then allowed communities to assemble. As previously shown, initial host diversity and resource supply determined the trajectory of host community assembly, altering post-assembly host species richness, richness-independent host phylogenetic diversity, and colonization by exotic host species. Overall, host richness predicted parasite richness, and as predicted, this effect was moderated by exotic abundance-communities dominated by exotic species exhibited a stronger positive relationship between post-assembly host and parasite richness. Ultimately, these results suggest that, by modulating parasite transmission, community assembly can modify the relationship between host and parasite richness. These results thus provide a novel mechanism to explain how global environmental change can generate contingencies in a fundamental ecological relationship-the positive relationship between host and parasite richness.
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Affiliation(s)
- Fletcher W Halliday
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Robert W Heckman
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Peter A Wilfahrt
- Environment, Ecology and Energy Program, University of North Carolina, Chapel Hill, NC, USA
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
| | - Charles E Mitchell
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Environment, Ecology and Energy Program, University of North Carolina, Chapel Hill, NC, USA
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Karasov TL, Shirsekar G, Schwab R, Weigel D. What natural variation can teach us about resistance durability. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:89-98. [PMID: 32535454 DOI: 10.1016/j.pbi.2020.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/08/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Friberg H, Persson P, Jensen DF, Bergkvist G. Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil. FEMS Microbiol Lett 2020; 366:5561442. [PMID: 31504475 PMCID: PMC6759068 DOI: 10.1093/femsle/fnz189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/02/2019] [Indexed: 12/02/2022] Open
Abstract
Agricultural practices like tillage and cropping sequence have profound influence on soil-living and plant-associated fungi, and thereby on plant growth. In a field experiment, we studied the effects of preceding crop and tillage on fungal communities in the soil and on young winter wheat roots in relation to plant winter survival and grain yield. We hypothesized that plant performance and fungal communities (described by amplicon sequencing) differ depending on tillage system and preceding crop; that the effect of preceding crop differs depending on tillage system, and that differences in fungal communities are reflected in plant performance. In line with our hypotheses, effects of preceding crop on plant growth and fungal communities on plant roots and in soil were more pronounced under non-inversion tillage than under inversion tillage (ploughing). Fungal communities on plant roots in treatments with low winter survival were different from those with better survival. In soil, several fungal OTUs (operational taxonomic units) differed significantly between tillage systems. OTUs representing putative plant pathogens were either more abundant (Parastagonospora sp._27) or less abundant (Fusarium culmorum/graminearum_5) after non-inversion tillage. Our findings highlight the influence of cultural practices on fungal communities and thereby on plant health and yield.
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Affiliation(s)
- Hanna Friberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala , Sweden
| | - Paula Persson
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, P.O. Box 7043, 75007 Uppsala , Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala , Sweden
| | - Göran Bergkvist
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, P.O. Box 7043, 75007 Uppsala , Sweden
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Drivers of Foliar Fungal Endophytic Communities of Kudzu (Pueraria montana var. lobata) in the Southeast United States. DIVERSITY 2020. [DOI: 10.3390/d12050185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fungal endophytes play important roles in plant fitness and plant–microbe interactions. Kudzu (Pueraria montana var. lobata) is a dominant, abundant, and highly aggressive invasive plant in the Southeast United States. Kudzu serves as a pathogen reservoir that impacts economically important leguminous crops. We conducted the first investigations on kudzu fungal endophytes (Illumina MiSeq—ITS2) to elucidate drivers of endophytic communities across the heart of the invasive range in the Southeast United States (TN, MS, AL, GA). We tested the impacts of multiple environmental parameters (Chlorophyll, NO3−, K+, soil pH, leaf area, host genotype, traffic intensity, and geographic location) on foliar endophyte communities. Endophytic communities were diverse and structured by many factors in our PerMANOVA analyses, but location, genotype, and traffic (proxy for pollution) were the strongest drivers of community composition (R2 = 0.152, p < 0.001, R2 = 0.129, p < 0.001, and R2 = 0.126, p < 0.001, respectively). Further, we examined the putative ecological interactions between endophytic fungi and plant pathogens. We identify numerous OTUs that are positively and strongly associated with pathogen occurrence, largely within the families Montagnulaceae and Tremellales incertae sedis. Taken together, these data suggest location, host genetics and local pollution play instrumental roles in structuring communities, and integrative plant management must consider these factors when developing management strategies.
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Gómez-Gallego M, LeBoldus JM, Bader MKF, Hansen E, Donaldson L, Williams NM. Contrasting the Pathogen Loads in Co-Existing Populations of Phytophthora pluvialis and Nothophaeocryptopus gaeumannii in Douglas Fir Plantations in New Zealand and the Pacific Northwest United States. PHYTOPATHOLOGY 2019; 109:1908-1921. [PMID: 31282283 DOI: 10.1094/phyto-12-18-0479-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The emergence of Phytophthora pluvialis as a foliar pathogen of Douglas fir in New Zealand and the Pacific Northwest United States has raised questions about its interaction with the widespread Swiss needle cast (SNC) disease. During Spring 2017, we repeatedly sampled 30 trees along an environmental gradient in each region and 292 additional trees in a longitudinal transect to assess the P. pluvialis epidemic and the association between P. pluvialis and Nothophaeocryptopus gaeumannii, which are causal agents of SNC. Both pathogens were consistently more abundant in the host's exotic environment in New Zealand. In both areas, the two pathogens co-exist in different spatial scales for regions and needles. The relative abundance of both pathogens was negatively correlated in the Pacific Northwest, where both presumably have co-existed for longer. Our findings confirmed the interaction of P. pluvialis and N. gaeumannii as foliar pathogens of Douglas fir and suggest a within-site spatial variation in the Pacific Northwest.
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Affiliation(s)
- Mireia Gómez-Gallego
- School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- New Zealand Forest Research Institute (Scion), Rotorua 3046, New Zealand
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | | | - Everett Hansen
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Lloyd Donaldson
- New Zealand Forest Research Institute (Scion), Rotorua 3046, New Zealand
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Makiola A, Dickie IA, Holdaway RJ, Wood JR, Orwin KH, Glare TR. Land use is a determinant of plant pathogen alpha‐ but not beta‐diversity. Mol Ecol 2019; 28:3786-3798. [DOI: 10.1111/mec.15177] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Andreas Makiola
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Université Bourgogne Franche‐Comté Dijon France
- Bio‐Protection Research Centre Lincoln University Lincoln New Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological Sciences University of Canterbury Christchurch New Zealand
| | | | - Jamie R. Wood
- Manaaki Whenua – Landcare Research Lincoln New Zealand
| | - Kate H. Orwin
- Manaaki Whenua – Landcare Research Lincoln New Zealand
| | - Travis R. Glare
- Bio‐Protection Research Centre Lincoln University Lincoln New Zealand
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Wong JWH, Plett JM. Root renovation: how an improved understanding of basic root biology could inform the development of elite crops that foster sustainable soil health. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:597-612. [PMID: 31029179 DOI: 10.1071/fp18200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 03/08/2019] [Indexed: 05/24/2023]
Abstract
A major goal in agricultural research is to develop 'elite' crops with stronger, resilient root systems. Within this context, breeding practices have focussed on developing plant varieties that are, primarily, able to withstand pathogen attack and, secondarily, able to maximise plant productivity. Although great strides towards breeding disease-tolerant or -resistant root stocks have been made, this has come at a cost. Emerging studies in certain crop species suggest that domestication of crops, together with soil management practices aimed at improving plant yield, may hinder beneficial soil microbial association or reduce microbial diversity in soil. To achieve more sustainable management of agricultural lands, we must not only shift our soil management practices but also our breeding strategy to include contributions from beneficial microbes. For this latter point, we need to advance our understanding of how plants communicate with, and are able to differentiate between, microbes of different lifestyles. Here, we present a review of the key findings on belowground plant-microbial interactions that have been made over the past decade, with a specific focus on how plants and microbes communicate. We also discuss the currently unresolved questions in this area, and propose plausible ways to use currently available research and integrate fast-emerging '-omics' technologies to tackle these questions. Combining past and developing research will enable the development of new crop varieties that will have new, value-added phenotypes belowground.
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Affiliation(s)
- Johanna W-H Wong
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; and Corresponding author.
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Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health. FORESTS 2019. [DOI: 10.3390/f10010042] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
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Makiola A, Dickie IA, Holdaway RJ, Wood JR, Orwin KH, Lee CK, Glare TR. Biases in the metabarcoding of plant pathogens using rust fungi as a model system. Microbiologyopen 2018; 8:e00780. [PMID: 30585441 PMCID: PMC6612544 DOI: 10.1002/mbo3.780] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species.
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Affiliation(s)
- Andreas Makiola
- Agroécologie, AgroSup Dijon, INRAUniversité Bourgogne, Université Bourgogne Franche‐ComtéDijonFrance,Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyNew Zealand
| | | | - Jamie R. Wood
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Kate H. Orwin
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Charles K. Lee
- Waikato DNA Sequencing Facility, School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Travis R. Glare
- Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
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Semchenko M, Leff JW, Lozano YM, Saar S, Davison J, Wilkinson A, Jackson BG, Pritchard WJ, De Long JR, Oakley S, Mason KE, Ostle NJ, Baggs EM, Johnson D, Fierer N, Bardgett RD. Fungal diversity regulates plant-soil feedbacks in temperate grassland. SCIENCE ADVANCES 2018; 4:eaau4578. [PMID: 30498781 PMCID: PMC6261650 DOI: 10.1126/sciadv.aau4578] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/25/2018] [Indexed: 05/18/2023]
Abstract
Feedbacks between plants and soil microbial communities play an important role in vegetation dynamics, but the underlying mechanisms remain unresolved. Here, we show that the diversity of putative pathogenic, mycorrhizal, and saprotrophic fungi is a primary regulator of plant-soil feedbacks across a broad range of temperate grassland plant species. We show that plant species with resource-acquisitive traits, such as high shoot nitrogen concentrations and thin roots, attract diverse communities of putative fungal pathogens and specialist saprotrophs, and a lower diversity of mycorrhizal fungi, resulting in strong plant growth suppression on soil occupied by the same species. Moreover, soil properties modulate feedbacks with fertile soils, promoting antagonistic relationships between soil fungi and plants. This study advances our capacity to predict plant-soil feedbacks and vegetation dynamics by revealing fundamental links between soil properties, plant resource acquisition strategies, and the diversity of fungal guilds in soil.
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Affiliation(s)
- Marina Semchenko
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Corresponding author.
| | - Jonathan W. Leff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Yudi M. Lozano
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Sirgi Saar
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Institute of Ecology and Earth Sciences, The University of Tartu, Lai 40, 51005 Tartu, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, The University of Tartu, Lai 40, 51005 Tartu, Estonia
| | - Anna Wilkinson
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Benjamin G. Jackson
- The Global Academy of Agriculture and Food Security, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
| | - William J. Pritchard
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jonathan R. De Long
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB Wageningen, Netherlands
| | - Simon Oakley
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
| | - Kelly E. Mason
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
| | - Nicholas J. Ostle
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Elizabeth M. Baggs
- The Global Academy of Agriculture and Food Security, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
| | - David Johnson
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Richard D. Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Kazartsev I, Shorohova E, Kapitsa E, Kushnevskaya H. Decaying Picea abies log bark hosts diverse fungal communities. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2017.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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de Souza ÉSDC, do Vale HMM, Pereira Carvalho RDC, Soares WRDO, Miller RNG, Dianese JC. Infection by Uromyces euphorbiae: a trigger for the sporulation of endophytic Colletotrichum truncatum on the common host Euphorbia hirta. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1338-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Whitaker BK, Bauer JT, Bever JD, Clay K. Negative plant-phyllosphere feedbacks in native Asteraceae hosts - a novel extension of the plant-soil feedback framework. Ecol Lett 2017; 20:1064-1073. [PMID: 28677329 DOI: 10.1111/ele.12805] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/20/2017] [Accepted: 06/01/2017] [Indexed: 01/20/2023]
Abstract
Over the past 25 years, the plant-soil feedback (PSF) framework has catalyzed our understanding of how belowground microbiota impact plant fitness and species coexistence. Here, we apply a novel extension of this framework to microbiota associated with aboveground tissues, termed 'plant-phyllosphere feedback (PPFs)'. In parallel greenhouse experiments, rhizosphere and phyllosphere microbiota of con- and heterospecific hosts from four species were independently manipulated. In a third experiment, we tested the combined effects of soil and phyllosphere feedback under field conditions. We found that three of four species experienced weak negative PSF whereas, in contrast, all four species experienced strong negative PPFs. Field-based feedback estimates were highly negative for all four species, though variable in magnitude. Our results suggest that phyllosphere microbiota, like rhizosphere microbiota, can potentially mediate plant species coexistence via negative feedbacks. Extension of the PSF framework to the phyllosphere is needed to more fully elucidate plant-microbiota interactions.
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Affiliation(s)
- Briana K Whitaker
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St, Bloomington, IN, 47405-3700, USA
| | - Jonathan T Bauer
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St, Bloomington, IN, 47405-3700, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology, University of Kansas, Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047-7503, USA
| | - Keith Clay
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St, Bloomington, IN, 47405-3700, USA
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De Silva DD, Crous PW, Ades PK, Hyde KD, Taylor PW. Life styles of Colletotrichum species and implications for plant biosecurity. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.05.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Marsberg A, Kemler M, Jami F, Nagel JH, Postma‐Smidt A, Naidoo S, Wingfield MJ, Crous PW, Spatafora JW, Hesse CN, Robbertse B, Slippers B. Botryosphaeria dothidea: a latent pathogen of global importance to woody plant health. MOLECULAR PLANT PATHOLOGY 2017; 18:477-488. [PMID: 27682468 PMCID: PMC6638292 DOI: 10.1111/mpp.12495] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/19/2016] [Accepted: 09/24/2016] [Indexed: 05/26/2023]
Abstract
Botryosphaeria dothidea is the type species of Botryosphaeria (Botryosphaeriaceae, Botryosphaeriales). Fungi residing in this order are amongst the most widespread and important canker and dieback pathogens of trees worldwide, with B. dothidea one of the most common species on a large number of hosts. Its taxonomic circumscription has undergone substantial change in the past decade, making it difficult to interpret the large volume of literature linked to the name B. dothidea. This pathogen profile synthesizes the current understanding of B. dothidea pertaining to its distribution, host associations and role as a pathogen in managed and natural woody environments. The prolonged latent infection or endophytic phase is of particular importance, as it implies that the fungus can easily pass undetected by quarantine systems in traded living plants, fruits and other plant parts. Infections typically become obvious only under conditions of host stress, when disease symptoms develop. This study also considers the knowledge emerging from the recently sequenced B. dothidea genome, elucidating previously unknown aspects of the species, including mating and host infection strategies. Despite more than 150 years of research on B. dothidea, there is clearly much to be learned regarding this global tree pathogen. This is increasingly important given the stresses imposed on various woody hosts as a result of climate change. TAXONOMY Botryosphaeria dothidea (Moug. ex Fr) Ces. & De Not, 1863. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Botryosphaeriaceae, Genus Botryosphaeria, Species dothidea. HOST RANGE Confirmed on more than 24 host genera, including woody plants, such as Acacia (= Vachellia), Eucalyptus, Vitis and Pistachio. DISEASE SYMPTOMS Associated with twig, branch and stem cankers, tip and branch dieback, fruit rot, blue stain and plant death. USEFUL WEBSITES The Botryosphaeria site for detailed morphological descriptions (http://www.crem.fct.unl.pt/botryosphaeria_site/); Systematic Mycology and Microbiology Laboratory Fungal Database for all literature and associated hosts (https://nt.ars-grin.gov/fungaldatabases/); TreeBASE link for the combined ITS and TEF-1α tree (http://purl.org/phylo/treebase/phylows/study/TB2:S18906); DOE Joint Genome Institute, JGI Mycocosm for the Botryosphaeria dothidea genome (http://genome.jgi.doe.gov/Botdo1_1/Botdo1_1.home.html).
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Affiliation(s)
- Angelica Marsberg
- Department of GeneticsForestry and Agricultural Biotechnology Institute, University of PretoriaPrivate Bag x20, Hatfield 0028PretoriaSouth Africa
| | - Martin Kemler
- Department of GeneticsForestry and Agricultural Biotechnology Institute, University of PretoriaPrivate Bag x20, Hatfield 0028PretoriaSouth Africa
| | - Fahimeh Jami
- Department of Microbiology and Plant PathologyForestry and Agricultural Biotechnology Institute, University of PretoriaHatfield 0028PretoriaSouth Africa
| | - Jan H. Nagel
- Department of GeneticsForestry and Agricultural Biotechnology Institute, University of PretoriaPrivate Bag x20, Hatfield 0028PretoriaSouth Africa
| | - Alisa Postma‐Smidt
- Bioinformatics and Computational Biology UnitForestry and Agricultural Biotechnology Institute, University of PretoriaHatfield 0028PretoriaSouth Africa
| | - Sanushka Naidoo
- Department of GeneticsForestry and Agricultural Biotechnology Institute, University of PretoriaPrivate Bag x20, Hatfield 0028PretoriaSouth Africa
| | - Michael J. Wingfield
- Department of GeneticsForestry and Agricultural Biotechnology Institute, University of PretoriaPrivate Bag x20, Hatfield 0028PretoriaSouth Africa
| | - Pedro W. Crous
- Department of Microbiology and Plant PathologyForestry and Agricultural Biotechnology Institute, University of PretoriaHatfield 0028PretoriaSouth Africa
- CBS‐KNAW Fungal Biodiversity CentreUppsalalaan 8UtrechtCT3584the Netherlands
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Cordley Hall 2082Oregon State UniversityCorvallisOR97331‐2902USA
| | - Cedar N. Hesse
- US Department of AgricultureAgricultural Research ServiceCorvallisOR97331‐2902USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaMD20817USA
| | - Bernard Slippers
- Department of GeneticsForestry and Agricultural Biotechnology Institute, University of PretoriaPrivate Bag x20, Hatfield 0028PretoriaSouth Africa
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Tree Diseases as a Cause and Consequence of Interacting Forest Disturbances. FORESTS 2017. [DOI: 10.3390/f8050147] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Aguilar‐Trigueros CA, Rillig MC. Effect of different root endophytic fungi on plant community structure in experimental microcosms. Ecol Evol 2016; 6:8149-8158. [PMID: 27878084 PMCID: PMC5108266 DOI: 10.1002/ece3.2416] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/25/2023] Open
Abstract
Understanding the effects of root-associated microbes in explaining plant community patterns represents a challenge in community ecology. Although typically overlooked, several lines of evidence point out that nonmycorrhizal, root endophytic fungi in the Ascomycota may have the potential to drive changes in plant community ecology given their ubiquitous presence, wide host ranges, and plant species-specific fitness effects. Thus, we experimentally manipulated the presence of root endophytic fungal species in microcosms and measured its effects on plant communities. Specifically, we tested whether (1) three different root endophyte species can modify plant community structure; (2) those changes can also modified the way plant respond to different soil types; and (3) the effects are modified when all the fungi are present. As a model system, we used plant and fungal species that naturally co-occur in a temperate grassland. Further, the soil types used in our experiment reflected a strong gradient in soil texture that has been shown to drive changes in plant and fungal community structure in the field. Results showed that each plant species responded differently to infection, resulting in distinct patterns of plant community structure depending on the identity of the fungus present. Those effects depended on the soil type. For example, large positive effects due to presence of the fungi were able to compensate for less nutrients levels in one soil type. Further, host responses when all three fungi were present were different from the ones observed in single fungal inoculations, suggesting that endophyte-endophyte interactions may be important in structuring plant communities. Overall, these results indicate that plant responses to changes in the species identity of nonmycorrhizal fungal community species and their interactions can modify plant community structure.
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Affiliation(s)
- Carlos A. Aguilar‐Trigueros
- Plant EcologyInstitut für BiologieFreie Universität BerlinBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity ResearchBerlinGermany
| | - Matthias C. Rillig
- Plant EcologyInstitut für BiologieFreie Universität BerlinBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity ResearchBerlinGermany
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Card S, Johnson L, Teasdale S, Caradus J. Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents. FEMS Microbiol Ecol 2016; 92:fiw114. [PMID: 27222223 DOI: 10.1093/femsec/fiw114] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2016] [Indexed: 11/14/2022] Open
Abstract
Endophytes associate with the majority of plant species found in natural and managed ecosystems. They are regarded as extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Fossil records of endophytes date back more than 400 million years, implicating these microorganisms in host plant adaptation to habitat transitions. However, it is only recently that endophytes, and their bioactive products, have received meaningful attention from the scientific community. The benefits some endophytes can confer on their hosts include plant growth promotion and survival through the inhibition of pathogenic microorganisms and invertebrate pests, the removal of soil contaminants, improved tolerance of low fertility soils, and increased tolerance of extreme temperatures and low water availability. Endophytes are extremely diverse and can exhibit many different biological behaviours. Not all endophyte technologies have been successfully commercialised. Of interest in the development of the next generation of plant protection products is how much of this is due to the biology of the particular endophytic microorganism. In this review, we highlight selected case studies of endophytes and discuss their lifestyles and behavioural traits, and discuss how these factors contribute towards their effectiveness as biological control agents.
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Affiliation(s)
- Stuart Card
- AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Linda Johnson
- AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Suliana Teasdale
- AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand
| | - John Caradus
- Grasslanz Technology Limited, Private Bag 11008, Palmerston North 4442, New Zealand
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Shaw MW, Emmanuel CJ, Emilda D, Terhem RB, Shafia A, Tsamaidi D, Emblow M, van Kan JAL. Analysis of Cryptic, Systemic Botrytis Infections in Symptomless Hosts. FRONTIERS IN PLANT SCIENCE 2016; 7:625. [PMID: 27242829 PMCID: PMC4861902 DOI: 10.3389/fpls.2016.00625] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/24/2016] [Indexed: 05/05/2023]
Abstract
Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. Botrytis cinerea and Botrytis pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.
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Affiliation(s)
- Michael W. Shaw
- School of Agriculture, Policy and Development, University of Reading, WhiteknightsReading, UK
| | - Christy J. Emmanuel
- School of Agriculture, Policy and Development, University of Reading, WhiteknightsReading, UK
| | - Deni Emilda
- Laboratory of Phytopathology, Wageningen UniversityWageningen, Netherlands
| | - Razak B. Terhem
- Laboratory of Phytopathology, Wageningen UniversityWageningen, Netherlands
| | - Aminath Shafia
- School of Agriculture, Policy and Development, University of Reading, WhiteknightsReading, UK
| | - Dimitra Tsamaidi
- School of Agriculture, Policy and Development, University of Reading, WhiteknightsReading, UK
| | - Mark Emblow
- School of Agriculture, Policy and Development, University of Reading, WhiteknightsReading, UK
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen UniversityWageningen, Netherlands
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Solis MJL, Dela Cruz TE, Schnittler M, Unterseher M. The diverse community of leaf-inhabiting fungal endophytes from Philippine natural forests reflects phylogenetic patterns of their host plant species Ficus benjamina, F. elastica and F. religiosa. MYCOSCIENCE 2016. [DOI: 10.1016/j.myc.2015.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Swett CL, Kirkpatrick SC, Gordon TR. Evidence for a Hemibiotrophic Association of the Pitch Canker Pathogen Fusarium circinatum with Pinus radiata. PLANT DISEASE 2016; 100:79-84. [PMID: 30688583 DOI: 10.1094/pdis-03-15-0270-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fusarium circinatum can be a cause of mortality in pine seedlings but it is also possible for infected seedlings to remain symptomless. The results of this study documented a biotrophic phase in symptomless Pinus radiata seedlings that can persist for at least 52 weeks. A strain of F. circinatum, transformed to express the green fluorescent protein, was observed to grow intercellularly in the root cortex, with no evidence of damage to surrounding cells. Under experimental conditions, shoot symptoms developed only following collar infection, and root deterioration was seen only in plants that first expressed aboveground symptoms. This sequence of events implies that damage to the root system was a secondary consequence of girdling. If so, root symptoms may not reliably detect seedlings infected by F. circinatum. Supplemental mineral nutrition increased the incidence of infection and symptom development in seedlings but some infected plants remained symptomless, precluding the use of this approach to detect infected seedlings. Overall, our findings suggest that the ecological activities of F. circinatum may not be limited to a necrotrophic association with pine trees. A more comprehensive understanding of the life history of this fungus may yield insights that contribute to more effective management of pitch canker.
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Affiliation(s)
- Cassandra L Swett
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park 20742
| | | | - Thomas R Gordon
- Department of Plant Pathology, University of California, Davis 95616
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Muggia L, Fleischhacker A, Kopun T, Grube M. Extremotolerant fungi from alpine rock lichens and their phylogenetic relationships. FUNGAL DIVERS 2015; 76:119-142. [PMID: 26877720 PMCID: PMC4739527 DOI: 10.1007/s13225-015-0343-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/06/2015] [Indexed: 01/23/2023]
Abstract
Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments. In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli, where they persist under the same stressful conditions as their hosts. Here we used a comprehensive sampling of lichen-associated fungi from an alpine habitat to assess their phylogenetic relationships with fungi previously known from other niches. The multilocus phylogenetic analyses suggest that most of the 248 isolates belong to the Chaetothyriomycetes and Dothideomycetes, while a minor fraction represents Sordariomycetes and Leotiomycetes. As many lichens also were infected by phenotypically distinct lichenicolous fungi of diverse lineages, it remains difficult to assess whether the culture isolates represent these fungi or are from additional cryptic, extremotolerant fungi within the thalli. Some of these strains represent yet undescribed lineages within Chaethothyriomycetes and Dothideomycetes, whereas other strains belong to genera of fungi, that are known as lichen colonizers, plant and human pathogens, rock-inhabiting fungi, parasites and saprotrophs. The symbiotic structures of the lichen thalli appear to be a shared habitat of phylogenetically diverse stress-tolerant fungi, which potentially benefit from the lichen niche in otherwise hostile habitats.
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Affiliation(s)
- Lucia Muggia
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria ; Department of Life Sciences, Università degli Studi di Trieste, Via Valerio 12/2, 34128 Trieste, Italy
| | | | - Theodora Kopun
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
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Schwessinger B, Bart R, Krasileva KV, Coaker G. Focus issue on plant immunity: from model systems to crop species. FRONTIERS IN PLANT SCIENCE 2015; 6:195. [PMID: 25859255 PMCID: PMC4374389 DOI: 10.3389/fpls.2015.00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/11/2015] [Indexed: 05/10/2023]
Affiliation(s)
- Benjamin Schwessinger
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute and Physical Biosciences DivisionBerkeley, CA, USA
- *Correspondence: Benjamin Schwessinger and Gitta Coaker, ;
| | - Rebecca Bart
- Donald Danforth Plant Science CenterSt. Louis, MO, USA
| | - Ksenia V. Krasileva
- The Genome Analysis Centre, Norwich Research ParkNorwich, UK
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
| | - Gitta Coaker
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
- *Correspondence: Benjamin Schwessinger and Gitta Coaker, ;
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