Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds
Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.559728/full |
| _version_ | 1828523517413425152 |
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| author | Mengying Wang Alexander W. Eyre Michael R. Thon Yeonyee Oh Ralph A. Dean |
| author_facet | Mengying Wang Alexander W. Eyre Michael R. Thon Yeonyee Oh Ralph A. Dean |
| author_sort | Mengying Wang |
| collection | DOAJ |
| description | Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents. |
| first_indexed | 2024-12-11T20:29:09Z |
| format | Article |
| id | doaj.art-b2eba79274d8431a9c652d2ed9f7125b |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T20:29:09Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-b2eba79274d8431a9c652d2ed9f7125b2022-12-22T00:51:52ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-09-011110.3389/fmicb.2020.559728559728Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From SeedsMengying Wang0Alexander W. Eyre1Michael R. Thon2Yeonyee Oh3Ralph A. Dean4Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United StatesFungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United StatesSpanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Villamayor, SpainFungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United StatesFungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United StatesMicrobes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.https://www.frontiersin.org/article/10.3389/fmicb.2020.559728/fullriceseed and seedlingmicrobiomediversitydriving factors |
| spellingShingle | Mengying Wang Alexander W. Eyre Michael R. Thon Yeonyee Oh Ralph A. Dean Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds Frontiers in Microbiology rice seed and seedling microbiome diversity driving factors |
| title | Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds |
| title_full | Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds |
| title_fullStr | Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds |
| title_full_unstemmed | Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds |
| title_short | Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds |
| title_sort | dynamic changes in the microbiome of rice during shoot and root growth derived from seeds |
| topic | rice seed and seedling microbiome diversity driving factors |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2020.559728/full |
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