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Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype

Fungal endophytes can influence production and post-harvest challenges in carrot, though the identity of these microbes as well as factors affecting their composition have not yet been determined, which prevents growers from managing these organisms to improve crop performance. Consequently, we char...

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Autores principales: Abdelrazek, Sahar, Choudhari, Sulbha, Thimmapuram, Jyothi, Simon, Philipp, Colley, Micaela, Mengiste, Tesfaye, Hoagland, Lori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426841/
https://www.ncbi.nlm.nih.gov/pubmed/32792547
http://dx.doi.org/10.1038/s41598-020-70683-x
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author Abdelrazek, Sahar
Choudhari, Sulbha
Thimmapuram, Jyothi
Simon, Philipp
Colley, Micaela
Mengiste, Tesfaye
Hoagland, Lori
author_facet Abdelrazek, Sahar
Choudhari, Sulbha
Thimmapuram, Jyothi
Simon, Philipp
Colley, Micaela
Mengiste, Tesfaye
Hoagland, Lori
author_sort Abdelrazek, Sahar
collection PubMed
description Fungal endophytes can influence production and post-harvest challenges in carrot, though the identity of these microbes as well as factors affecting their composition have not yet been determined, which prevents growers from managing these organisms to improve crop performance. Consequently, we characterized the endophytic mycobiome in the taproots of three carrot genotypes that vary in resistance to two pathogens grown in a trial comparing organic and conventional crop management using Illumina sequencing of the internal transcribed spacer (ITS) gene. A total of 1,480 individual operational taxonomic units (OTUs) were identified. Most were consistent across samples, indicating that they are part of a core mycobiome, though crop management influenced richness and diversity, likely in response to differences in soil properties. There were also differences in individual OTUs among genotypes and the nematode resistant genotype was most responsive to management system indicating that it has greater control over its endophytic mycobiome, which could potentially play a role in resistance. Members of the Ascomycota were most dominant, though the exact function of most taxa remains unclear. Future studies aimed at overcoming difficulties associated with isolating fungal endophytes are needed to identify these microbes at the species level and elucidate their specific functional roles.
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spelling pubmed-74268412020-08-14 Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype Abdelrazek, Sahar Choudhari, Sulbha Thimmapuram, Jyothi Simon, Philipp Colley, Micaela Mengiste, Tesfaye Hoagland, Lori Sci Rep Article Fungal endophytes can influence production and post-harvest challenges in carrot, though the identity of these microbes as well as factors affecting their composition have not yet been determined, which prevents growers from managing these organisms to improve crop performance. Consequently, we characterized the endophytic mycobiome in the taproots of three carrot genotypes that vary in resistance to two pathogens grown in a trial comparing organic and conventional crop management using Illumina sequencing of the internal transcribed spacer (ITS) gene. A total of 1,480 individual operational taxonomic units (OTUs) were identified. Most were consistent across samples, indicating that they are part of a core mycobiome, though crop management influenced richness and diversity, likely in response to differences in soil properties. There were also differences in individual OTUs among genotypes and the nematode resistant genotype was most responsive to management system indicating that it has greater control over its endophytic mycobiome, which could potentially play a role in resistance. Members of the Ascomycota were most dominant, though the exact function of most taxa remains unclear. Future studies aimed at overcoming difficulties associated with isolating fungal endophytes are needed to identify these microbes at the species level and elucidate their specific functional roles. Nature Publishing Group UK 2020-08-13 /pmc/articles/PMC7426841/ /pubmed/32792547 http://dx.doi.org/10.1038/s41598-020-70683-x Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Abdelrazek, Sahar
Choudhari, Sulbha
Thimmapuram, Jyothi
Simon, Philipp
Colley, Micaela
Mengiste, Tesfaye
Hoagland, Lori
Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
title Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
title_full Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
title_fullStr Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
title_full_unstemmed Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
title_short Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
title_sort changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426841/
https://www.ncbi.nlm.nih.gov/pubmed/32792547
http://dx.doi.org/10.1038/s41598-020-70683-x
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