The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em>
Powdery mildew disease caused by <i>Oidium neolycopersici</i> is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing s...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-05-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/8/5/404 |
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| author | Afeez Adesina Adedayo Ayomide Emmanuel Fadiji Olubukola Oluranti Babalola |
| author_facet | Afeez Adesina Adedayo Ayomide Emmanuel Fadiji Olubukola Oluranti Babalola |
| author_sort | Afeez Adesina Adedayo |
| collection | DOAJ |
| description | Powdery mildew disease caused by <i>Oidium neolycopersici</i> is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing shotgun metagenomics. In this study, we assess how the health status of a tomato plant affects the diversity of the rhizosphere microbial community. We collected soil samples from the rhizosphere of healthy (HR) and diseased (DR; powdery mildew infected) tomatoes, alongside bulk soil (BR), extracted DNA, and did sequencing using shotgun metagenomics. Our results demonstrated that the rhizosphere microbiome alongside some specific functions were abundant in HR followed by DR and bulk soil (BR) in the order HR > DR > BR. We found eighteen (18) bacterial phyla abundant in HR, including <i>Actinobacteria</i>, <i>Acidobacteria</i>, <i>Aquificae</i>, <i>Bacteroidetes</i>, etc. The dominant fungal phyla include; <i>Ascomycota</i> and <i>Basidiomycota</i>, while the prominent archaeal phyla are <i>Thaumarchaeota</i>, <i>Crenarchaeota</i>, and <i>Euryarchaeota</i>. Three (3) bacteria phyla dominated the DR samples; <i>Bacteroidetes</i>, <i>Gemmatimonadetes,</i> and <i>Thermotoga</i>. Our result also employed the SEED subsystem and revealed that the metabolic pathways involved were abundant in HR. The α-diversity demonstrates that there is no significant difference among the rhizosphere microbiomes across the sites, while β-diversity demonstrated a significant difference. |
| first_indexed | 2024-03-10T03:47:00Z |
| format | Article |
| id | doaj.art-0d54c19d4e334292817c7f7b1a5e00dc |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-10T03:47:00Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj.art-0d54c19d4e334292817c7f7b1a5e00dc2023-11-23T11:16:45ZengMDPI AGHorticulturae2311-75242022-05-018540410.3390/horticulturae8050404The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em>Afeez Adesina Adedayo0Ayomide Emmanuel Fadiji1Olubukola Oluranti Babalola2Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South AfricaFood Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South AfricaFood Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South AfricaPowdery mildew disease caused by <i>Oidium neolycopersici</i> is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing shotgun metagenomics. In this study, we assess how the health status of a tomato plant affects the diversity of the rhizosphere microbial community. We collected soil samples from the rhizosphere of healthy (HR) and diseased (DR; powdery mildew infected) tomatoes, alongside bulk soil (BR), extracted DNA, and did sequencing using shotgun metagenomics. Our results demonstrated that the rhizosphere microbiome alongside some specific functions were abundant in HR followed by DR and bulk soil (BR) in the order HR > DR > BR. We found eighteen (18) bacterial phyla abundant in HR, including <i>Actinobacteria</i>, <i>Acidobacteria</i>, <i>Aquificae</i>, <i>Bacteroidetes</i>, etc. The dominant fungal phyla include; <i>Ascomycota</i> and <i>Basidiomycota</i>, while the prominent archaeal phyla are <i>Thaumarchaeota</i>, <i>Crenarchaeota</i>, and <i>Euryarchaeota</i>. Three (3) bacteria phyla dominated the DR samples; <i>Bacteroidetes</i>, <i>Gemmatimonadetes,</i> and <i>Thermotoga</i>. Our result also employed the SEED subsystem and revealed that the metabolic pathways involved were abundant in HR. The α-diversity demonstrates that there is no significant difference among the rhizosphere microbiomes across the sites, while β-diversity demonstrated a significant difference.https://www.mdpi.com/2311-7524/8/5/404plant microbiomesplant–rhizobiome interactionpowdery mildewSEED subsystemshotgun sequencingtomato |
| spellingShingle | Afeez Adesina Adedayo Ayomide Emmanuel Fadiji Olubukola Oluranti Babalola The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em> Horticulturae plant microbiomes plant–rhizobiome interaction powdery mildew SEED subsystem shotgun sequencing tomato |
| title | The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em> |
| title_full | The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em> |
| title_fullStr | The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em> |
| title_full_unstemmed | The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em> |
| title_short | The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with <em>Solanum lycopersicum</em> |
| title_sort | effects of plant health status on the community structure and metabolic pathways of rhizosphere microbial communities associated with em solanum lycopersicum em |
| topic | plant microbiomes plant–rhizobiome interaction powdery mildew SEED subsystem shotgun sequencing tomato |
| url | https://www.mdpi.com/2311-7524/8/5/404 |
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