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Adeyemo A, Schmidt-Heydt M. Expansion of the multi-locus gene alignment approach to improve identification of the fungal species Alternaria alternata. Int J Food Microbiol 2024; 421:110746. [PMID: 38917488 DOI: 10.1016/j.ijfoodmicro.2024.110746] [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: 12/27/2023] [Revised: 04/19/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Alternaria alternata is part of a genus comprised of over 600 different species that occur all over the world and cause damage to humans, plants and thereby to the economy. Yet, even though some species are causing tremendous issues, the past years have shown that assigning newly found isolates to known species was rather inconsistent. Most identifications are usually done on the basis of spore morphology, chemotype and molecular markers. In this work we used strains isolated from the wild as well as commercial strains of the DSMZ (German collection of microorganisms and cell cultures) as a reference, to show, that the variation within the Alternaria alternata species is comparable to the variation between different species of the genus Alternaria in regards to spore morphology and chemotype. We compared the different methods of identification and discerned the concatenation of multiple molecular markers as the deciding factor for better identification. Up until this point, usually a concatenation of two or three traditional molecular markers was used. Some of those markers being stronger some weaker. We show that the concatenation of five molecular markers improves the likeliness of a correct assignment, thus a better distinction between the different Alternaria species.
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Affiliation(s)
- Adetoye Adeyemo
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Karlsruhe, Germany.
| | - Markus Schmidt-Heydt
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Karlsruhe, Germany.
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Apangu GP, Frisk CA, Petch GM, Muggia L, Pallavicini A, Hanson M, Skjøth CA. Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK. AEROBIOLOGIA 2022; 38:457-481. [PMID: 36471880 PMCID: PMC9715499 DOI: 10.1007/s10453-022-09760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/28/2022] [Indexed: 05/05/2023]
Abstract
UNLABELLED Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09760-9.
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Affiliation(s)
- Godfrey Philliam Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, AL5 2JQ Hertfordshire UK
| | - Carl Alexander Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Geoffrey M. Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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Mackin HC, Shek KL, Thornton TE, Evens KC, Hallett LM, McGuire KL, DeMarche ML, Roy BA. The 'black box' of plant demography: how do seed type, climate and seed fungal communities affect grass seed germination? THE NEW PHYTOLOGIST 2021; 231:2319-2332. [PMID: 34091913 DOI: 10.1111/nph.17532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Demographic studies measure drivers of plant fecundity including seed production and survival, but few address both abiotic and biotic drivers of germination such as variation in climate among sites, population density, maternal plants, seed type and fungal pathogen abundance. We examined germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed populations were sourced across environmental gradients. We tested germination and used high-throughput sequencing to characterize seed fungal community structure. For F. roemeri, maternal plants significantly influenced germination as did climate and pathogens; germination increased from wetter, cooler sites. For D. californica, the main drivers of germination were maternal plant, seed type and pathogens; on average, more chasmogamous seeds germinated. Fungal communities depended largely on seed type, with fewer fungi associated with cleistogamous seeds, but the communities also depended on site factors such as vapor pressure deficit, plant density and whether the seeds had germinated. Putative pathogens that were negatively correlated with germination were more abundant for both D. californica and F. roemeri chasmogamous seeds than D. californica cleistogamous seeds. In D. californica, cleistogamous and chasmogamous seeds contain vastly different fungal communities.
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Affiliation(s)
- Hunter C Mackin
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Katherine L Shek
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Tiffany E Thornton
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Kayla C Evens
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Lauren M Hallett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Krista L McGuire
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
- Environmental Studies Program, University of Oregon, Eugene, OR, 97403, USA
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bitty A Roy
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
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Newcombe G, Fraser SJ, Ridout M, Busby PE. Leaf Endophytes of Populus trichocarpa Act as Pathogens of Neighboring Plant Species. Front Microbiol 2020; 11:573056. [PMID: 33281769 PMCID: PMC7705171 DOI: 10.3389/fmicb.2020.573056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/15/2020] [Indexed: 11/22/2022] Open
Abstract
The conventional definition of endophytes is that they do not cause disease, whereas pathogens do. Complicating this convention, however, is the poorly explored phenomenon that some microbes are endophytes in some plants but pathogens in others. Black cottonwood or poplar (Populus trichocarpa) and wheat (Triticum aestivum) are common wild and crop plants, respectively, in the Pacific Northwest USA. The former anchors wild, riparian communities, whereas the latter is an introduced domesticate of commercial importance in the region. We isolated Fusarium culmorum – a well-known pathogen of wheat causing both blight and rot – from the leaf of a black cottonwood tree in western Washington. The pathogenicity of this cottonwood isolate and of a wheat isolate of F. culmorum were compared by inoculating both cottonwood and wheat in a greenhouse experiment. We found that both the cottonwood and wheat isolates of F. culmorum significantly reduced the growth of wheat, whereas they had no impact on cottonwood growth. Our results demonstrate that the cottonwood isolate of F. culmorum is endophytic in one plant species but pathogenic in another. Using sequence-based methods, we found an additional 56 taxa in the foliar microbiome of cottonwood that matched the sequences of pathogens of other plants of the region. These sequence-based findings suggest, though they do not prove, that P. trichocarpa may host many additional pathogens of other plants.
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Affiliation(s)
- George Newcombe
- Department of Forest, Rangeland, and Fire Sciences, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Shannon J Fraser
- Department of Forest, Rangeland, and Fire Sciences, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Mary Ridout
- College of Agriculture and Life Sciences, University of Idaho Extension Washington County, Weiser, ID, United States
| | - Posy E Busby
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, OR, United States
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Mc Cargo PD, Iannone LJ, Soria M, Novas MV. Diversity of foliar endophytes in a dioecious wild grass and their interaction with the systemic Epichloë. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Fort T, Robin C, Capdevielle X, Delière L, Vacher C. Foliar fungal communities strongly differ between habitat patches in a landscape mosaic. PeerJ 2016; 4:e2656. [PMID: 27833817 PMCID: PMC5101609 DOI: 10.7717/peerj.2656] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Background Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores. Methods We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the Internal Transcribed Spacer 2 (ITS2) region. Results In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre. Discussion These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.
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Affiliation(s)
- Thomas Fort
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Cestas , France
| | - Cécile Robin
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Cestas , France
| | | | - Laurent Delière
- SAVE, UMR 1065, INRA, ISVV, Université de Bordeaux , Villenave d'Ornon , France
| | - Corinne Vacher
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Pessac , France
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Blaisdell GK, Roy BA, Pfeifer-Meister L, Bridgham SD. An exploration of hypotheses that explain herbivore and pathogen attack in restored plant communities. PLoS One 2015; 10:e0116650. [PMID: 25699672 PMCID: PMC4336146 DOI: 10.1371/journal.pone.0116650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/11/2014] [Indexed: 11/25/2022] Open
Abstract
Many hypotheses address the associations of plant community composition with natural enemies, including: (i) plant species diversity may reduce enemy attack, (ii) attack may increase as host abundance increases, (iii) enemy spillover may lead to increased attack on one host species due to transmission from another host species, or enemy dilution may lead to reduced attack on a host that would otherwise have more attack, (iv) physical characteristics of the plant community may influence attack, and (v) plant vigor may affect attack. Restoration experiments with replicated plant communities provide an exceptional opportunity to explore these hypotheses. To explore the relative predictive strengths of these related hypotheses and to investigate the potential effect of several restoration site preparation techniques, we surveyed arthropod herbivore and fungal pathogen attack on the six most common native plant species in a restoration experiment. Multi-model inference revealed a weak but consistent negative correlation with pathogen attack and host diversity across the plant community, and no correlation between herbivory and host diversity. Our analyses also revealed host species-specific relationships between attack and abundance of the target host species, other native plant species, introduced plant species, and physical community characteristics. We found no relationship between enemy attack and plant vigor. We found minimal differences in plant community composition among several diverse site preparation techniques, and limited effects of site preparation techniques on attack. The strongest associations of community characteristics with attack varied among plant species with no community-wide patterns, suggesting that no single hypothesis successfully predicts the dominant community-wide trends in enemy attack.
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Affiliation(s)
- G. Kai Blaisdell
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Bitty A. Roy
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Laurel Pfeifer-Meister
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Scott D. Bridgham
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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