Fungal microbiome of barley grain revealed by NGS and mycological analysis
Introduction. Barley can be infected with a broad variety of fungi, which can cause considerable loss of crop yield and reduce the quality of grain. Modern vision on the geographical and ecological distribution and biodiversity of micromycetes has been established by traditional, cultivation-based m...
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| Format: | Article |
| Language: | English |
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Kemerovo State University
2020-10-01
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| Series: | Foods and Raw Materials |
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| Online Access: | http://jfrm.ru/files/archive/16/Kazartsev.pdf |
| _version_ | 1818730574164000768 |
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| author | Kazartsev Igor A. Gagkaeva Tatiana Yu. Gavrilova Olga P. Gannibal Philipp B. |
| author_facet | Kazartsev Igor A. Gagkaeva Tatiana Yu. Gavrilova Olga P. Gannibal Philipp B. |
| author_sort | Kazartsev Igor A. |
| collection | DOAJ |
| description | Introduction. Barley can be infected with a broad variety of fungi, which can cause considerable loss of crop yield and reduce the quality of grain. Modern vision on the geographical and ecological distribution and biodiversity of micromycetes has been established by traditional, cultivation-based methods. However, more recently, molecular methods have shifted microbiological research to a new level, making it possible to investigate hidden taxonomical biodiversity.
Study objects and methods. For this study, we determined the fungal biome on the surface and inside of barley grains using the traditional mycological method and the contemporary molecular method, which employed DNA metabarcoding based on NGS (nextgeneration sequencing) of the ITS2 region. We analyzed five cultivars that were collected in two subsequent crop seasons (2014, 2015).
Results and discussion. DNA metabarcoding revealed 43 operational taxonomic units, while 17 taxa of genus or species level were recovered by the traditional method. DNA metabarcoding revealed several minor species and one predominant, presumably plantpathogenic Phaeosphaeria sp., which were not detected in the agar plate-based assay. Traditionally, Fusarium fungi were identified by mycological assay. However, the resolution of DNA metabarcoding was sufficient to determine main Fusarium groups divided by ability to produce toxic secondary metabolites. The combined list of Ascomycetes consisted of 15 genera, including 14 fungi identified to species level. The list of Basidiomycota derived from DNA metabarcoding data alone included 8 genera.
Conclusion. It was found that crop season predetermines the fungal community structure; mycobiota on the surface and inside of grain was significantly different. |
| first_indexed | 2024-12-17T23:03:57Z |
| format | Article |
| id | doaj.art-ddd1633249934553975d1e3a8acea7d8 |
| institution | Directory Open Access Journal |
| issn | 2308-4057 2310-9599 |
| language | English |
| last_indexed | 2024-12-17T23:03:57Z |
| publishDate | 2020-10-01 |
| publisher | Kemerovo State University |
| record_format | Article |
| series | Foods and Raw Materials |
| spelling | doaj.art-ddd1633249934553975d1e3a8acea7d82022-12-21T21:29:20ZengKemerovo State UniversityFoods and Raw Materials2308-40572310-95992020-10-018228629710.21603/2308-4057-2020-2-286-297Fungal microbiome of barley grain revealed by NGS and mycological analysisKazartsev Igor A. 0https://orcid.org/0000-0003-4500-0154Gagkaeva Tatiana Yu. 1https://orcid.org/0000-0002-3276-561XGavrilova Olga P. 2https://orcid.org/0000-0002-5350-3221Gannibal Philipp B. 3https://orcid.org/0000-0002-7944-5461All-Russian Institute of Plant Proteсtion, St. Petersburg, RussiaAll-Russian Institute of Plant Proteсtion, St. Petersburg, Russia; University of Tyumen, Tyumen, RussiaAll-Russian Institute of Plant Proteсtion, St. Petersburg, RussiaAll-Russian Institute of Plant Proteсtion, St. Petersburg, Russia; University of Tyumen, Tyumen, RussiaIntroduction. Barley can be infected with a broad variety of fungi, which can cause considerable loss of crop yield and reduce the quality of grain. Modern vision on the geographical and ecological distribution and biodiversity of micromycetes has been established by traditional, cultivation-based methods. However, more recently, molecular methods have shifted microbiological research to a new level, making it possible to investigate hidden taxonomical biodiversity. Study objects and methods. For this study, we determined the fungal biome on the surface and inside of barley grains using the traditional mycological method and the contemporary molecular method, which employed DNA metabarcoding based on NGS (nextgeneration sequencing) of the ITS2 region. We analyzed five cultivars that were collected in two subsequent crop seasons (2014, 2015). Results and discussion. DNA metabarcoding revealed 43 operational taxonomic units, while 17 taxa of genus or species level were recovered by the traditional method. DNA metabarcoding revealed several minor species and one predominant, presumably plantpathogenic Phaeosphaeria sp., which were not detected in the agar plate-based assay. Traditionally, Fusarium fungi were identified by mycological assay. However, the resolution of DNA metabarcoding was sufficient to determine main Fusarium groups divided by ability to produce toxic secondary metabolites. The combined list of Ascomycetes consisted of 15 genera, including 14 fungi identified to species level. The list of Basidiomycota derived from DNA metabarcoding data alone included 8 genera. Conclusion. It was found that crop season predetermines the fungal community structure; mycobiota on the surface and inside of grain was significantly different.http://jfrm.ru/files/archive/16/Kazartsev.pdfbarleyseed-borne fungiinfectionnext-generation sequencingrdnaalternariafusarium |
| spellingShingle | Kazartsev Igor A. Gagkaeva Tatiana Yu. Gavrilova Olga P. Gannibal Philipp B. Fungal microbiome of barley grain revealed by NGS and mycological analysis Foods and Raw Materials barley seed-borne fungi infection next-generation sequencing rdna alternaria fusarium |
| title | Fungal microbiome of barley grain revealed by NGS and mycological analysis |
| title_full | Fungal microbiome of barley grain revealed by NGS and mycological analysis |
| title_fullStr | Fungal microbiome of barley grain revealed by NGS and mycological analysis |
| title_full_unstemmed | Fungal microbiome of barley grain revealed by NGS and mycological analysis |
| title_short | Fungal microbiome of barley grain revealed by NGS and mycological analysis |
| title_sort | fungal microbiome of barley grain revealed by ngs and mycological analysis |
| topic | barley seed-borne fungi infection next-generation sequencing rdna alternaria fusarium |
| url | http://jfrm.ru/files/archive/16/Kazartsev.pdf |
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