High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity
The ecology of total fungal communities in grapevine is so far largely derived from studies on culture-dependent methods or cultivation-independent rDNA approaches. Sequencing the ribosomal RNA transcripts (rRNA) would rather reveal the functionally and metabolically active important taxa of the fungal community and provide insights into its activity in the wood. The present study investigated changes in the potentially active fungal communities of internal grapevine wood after Hot-Water Treatment (HWT) in planting material from Czech Republic and Spain at two different times during the propagation process and from two plant zones. We examined fungal communities using both traditional isolation into culture and high-throughput amplicon sequencing (HTAS) of the internal transcribed spacer 2 (ITS2) region in extracted total RNA. HTAS from metatranscriptomic RNA increased the resolution of the fungal community analysis and revealed a highly diverse mycobiota of grapevine wood compared to the traditional method. Fungal diversity differed between grapevine genotypes and showed a temporal variation over the vegetative period. Grapevine planting materials exhibited high fungal diversity after HWT, which demonstrates that the HWT process does not sterilize the internal wood of grapevine. HWT reduced the infection caused by fungal trunk disease pathogens but was not completely effective in eliminating their growth. This study provides important and practically useful insights into the dynamics of active fungal communities in hot-water treated plants, and represents the first study of active fungal communities on grapevine grafted plants by comparing traditional and next-generation sequencing methods.
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Format: | artículo biblioteca |
Language: | English |
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Elsevier
2018-12
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Subjects: | Endophytic fungi, Grapevine trunk diseases, ITS2, Metatranscriptomics, Mycobiota, NGS, Plant microbiome, |
Online Access: | http://hdl.handle.net/10261/192891 http://dx.doi.org/10.13039/501100000921 http://dx.doi.org/10.13039/100007652 http://dx.doi.org/10.13039/501100000780 |
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dig-icvv-es-10261-1928912019-11-06T08:18:09Z High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity Eichmeier, Ales Pečenka, Jakub Peňázová, Eliska Baránek, Miroslav Català-García, Santiago León, Maela Armengol, Josep Gramaje, David Ministry of Education, Youth and Sports (Czech Republic) CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) European Commission European Cooperation in Science and Technology Pečenka, Jakub [0000-0001-6195-7592] Armengol, Josep [0000-0003-3815-8578] Endophytic fungi Grapevine trunk diseases ITS2 Metatranscriptomics Mycobiota NGS Plant microbiome The ecology of total fungal communities in grapevine is so far largely derived from studies on culture-dependent methods or cultivation-independent rDNA approaches. Sequencing the ribosomal RNA transcripts (rRNA) would rather reveal the functionally and metabolically active important taxa of the fungal community and provide insights into its activity in the wood. The present study investigated changes in the potentially active fungal communities of internal grapevine wood after Hot-Water Treatment (HWT) in planting material from Czech Republic and Spain at two different times during the propagation process and from two plant zones. We examined fungal communities using both traditional isolation into culture and high-throughput amplicon sequencing (HTAS) of the internal transcribed spacer 2 (ITS2) region in extracted total RNA. HTAS from metatranscriptomic RNA increased the resolution of the fungal community analysis and revealed a highly diverse mycobiota of grapevine wood compared to the traditional method. Fungal diversity differed between grapevine genotypes and showed a temporal variation over the vegetative period. Grapevine planting materials exhibited high fungal diversity after HWT, which demonstrates that the HWT process does not sterilize the internal wood of grapevine. HWT reduced the infection caused by fungal trunk disease pathogens but was not completely effective in eliminating their growth. This study provides important and practically useful insights into the dynamics of active fungal communities in hot-water treated plants, and represents the first study of active fungal communities on grapevine grafted plants by comparing traditional and next-generation sequencing methods. This work was supported by Projects No. LD14051 from the Ministry of Education, Youth and Sports, Czech Republic covered by COST Action FA1303, and No. CZ.02.1.01/0.0/0.0/16_025/0007314 “Multidisciplinary research to increase application potential of nanomaterials in agricultural practice” from EFRR (Grant provider: Ministerstvo školství, mládeže a tělovýchovy České republiky (MŠMT). Access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum provided under the programme "Projects of Large Research, Development, and Innovations Infrastructures" (CESNET LM2015042), is greatly appreciated. David Gramaje was supported by the DOC-INIA program from the National Institute for Agronomic Research (INIA), co-funded by the European Social Fund. The authors are grateful for the technical assistance of Jesús Alfonso Crespo and Aitor Gavara Vidal. Peer reviewed 2019-10-18T10:19:14Z 2019-10-18T10:19:14Z 2018-12 artículo http://purl.org/coar/resource_type/c_6501 Fungal Ecology 36: 26-38 (2018) 1754-5048 http://hdl.handle.net/10261/192891 10.1016/j.funeco.2018.07.011 http://dx.doi.org/10.13039/501100000921 http://dx.doi.org/10.13039/100007652 http://dx.doi.org/10.13039/501100000780 en http://dx.doi.org/10.1016/j.funeco.2018.07.011 Sí none Elsevier |
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Endophytic fungi Grapevine trunk diseases ITS2 Metatranscriptomics Mycobiota NGS Plant microbiome Endophytic fungi Grapevine trunk diseases ITS2 Metatranscriptomics Mycobiota NGS Plant microbiome |
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Endophytic fungi Grapevine trunk diseases ITS2 Metatranscriptomics Mycobiota NGS Plant microbiome Endophytic fungi Grapevine trunk diseases ITS2 Metatranscriptomics Mycobiota NGS Plant microbiome Eichmeier, Ales Pečenka, Jakub Peňázová, Eliska Baránek, Miroslav Català-García, Santiago León, Maela Armengol, Josep Gramaje, David High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
description |
The ecology of total fungal communities in grapevine is so far largely derived from studies on culture-dependent methods or cultivation-independent rDNA approaches. Sequencing the ribosomal RNA transcripts (rRNA) would rather reveal the functionally and metabolically active important taxa of the fungal community and provide insights into its activity in the wood. The present study investigated changes in the potentially active fungal communities of internal grapevine wood after Hot-Water Treatment (HWT) in planting material from Czech Republic and Spain at two different times during the propagation process and from two plant zones. We examined fungal communities using both traditional isolation into culture and high-throughput amplicon sequencing (HTAS) of the internal transcribed spacer 2 (ITS2) region in extracted total RNA. HTAS from metatranscriptomic RNA increased the resolution of the fungal community analysis and revealed a highly diverse mycobiota of grapevine wood compared to the traditional method. Fungal diversity differed between grapevine genotypes and showed a temporal variation over the vegetative period. Grapevine planting materials exhibited high fungal diversity after HWT, which demonstrates that the HWT process does not sterilize the internal wood of grapevine. HWT reduced the infection caused by fungal trunk disease pathogens but was not completely effective in eliminating their growth. This study provides important and practically useful insights into the dynamics of active fungal communities in hot-water treated plants, and represents the first study of active fungal communities on grapevine grafted plants by comparing traditional and next-generation sequencing methods. |
author2 |
Ministry of Education, Youth and Sports (Czech Republic) |
author_facet |
Ministry of Education, Youth and Sports (Czech Republic) Eichmeier, Ales Pečenka, Jakub Peňázová, Eliska Baránek, Miroslav Català-García, Santiago León, Maela Armengol, Josep Gramaje, David |
format |
artículo |
topic_facet |
Endophytic fungi Grapevine trunk diseases ITS2 Metatranscriptomics Mycobiota NGS Plant microbiome |
author |
Eichmeier, Ales Pečenka, Jakub Peňázová, Eliska Baránek, Miroslav Català-García, Santiago León, Maela Armengol, Josep Gramaje, David |
author_sort |
Eichmeier, Ales |
title |
High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
title_short |
High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
title_full |
High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
title_fullStr |
High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
title_full_unstemmed |
High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
title_sort |
high-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity |
publisher |
Elsevier |
publishDate |
2018-12 |
url |
http://hdl.handle.net/10261/192891 http://dx.doi.org/10.13039/501100000921 http://dx.doi.org/10.13039/100007652 http://dx.doi.org/10.13039/501100000780 |
work_keys_str_mv |
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