Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost
Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.798476/full |
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| author | Ning Wang Ning Wang Huixiu Li Huixiu Li Bo Wang Jia Ding Jia Ding Yingjie Liu Yuquan Wei Yuquan Wei Ji Li Ji Li Guo-Chun Ding Guo-Chun Ding |
| author_facet | Ning Wang Ning Wang Huixiu Li Huixiu Li Bo Wang Jia Ding Jia Ding Yingjie Liu Yuquan Wei Yuquan Wei Ji Li Ji Li Guo-Chun Ding Guo-Chun Ding |
| author_sort | Ning Wang |
| collection | DOAJ |
| description | Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates. |
| first_indexed | 2024-04-11T17:11:36Z |
| format | Article |
| id | doaj.art-90a744d2dd1c4e5bafccb5f77b38decc |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T17:11:36Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-90a744d2dd1c4e5bafccb5f77b38decc2022-12-22T04:12:54ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-01-011210.3389/fmicb.2021.798476798476Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and CompostNing Wang0Ning Wang1Huixiu Li2Huixiu Li3Bo Wang4Jia Ding5Jia Ding6Yingjie Liu7Yuquan Wei8Yuquan Wei9Ji Li10Ji Li11Guo-Chun Ding12Guo-Chun Ding13Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaOrganic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaTangshan Normal University, Tangshan, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaOrganic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaOrganic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaOrganic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, ChinaBeijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, ChinaOrganic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, ChinaCompost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.https://www.frontiersin.org/articles/10.3389/fmicb.2021.798476/fullshotgun metagenomics16S rRNArhizospherecompostfunctional diversity |
| spellingShingle | Ning Wang Ning Wang Huixiu Li Huixiu Li Bo Wang Jia Ding Jia Ding Yingjie Liu Yuquan Wei Yuquan Wei Ji Li Ji Li Guo-Chun Ding Guo-Chun Ding Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost Frontiers in Microbiology shotgun metagenomics 16S rRNA rhizosphere compost functional diversity |
| title | Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost |
| title_full | Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost |
| title_fullStr | Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost |
| title_full_unstemmed | Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost |
| title_short | Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost |
| title_sort | taxonomic and functional diversity of rhizosphere microbiome recruited from compost synergistically determined by plant species and compost |
| topic | shotgun metagenomics 16S rRNA rhizosphere compost functional diversity |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.798476/full |
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