Nature Protocols
Abstract
Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called ‘Culturome’ (https://github.com/YongxinLiu/Culturome) and a graphical user interface web server (http://bailab.genetics.ac.cn/culturome/). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8–9 weeks.
| 论文编号: | DOI:10.1038/s41596-020-00444-7 |
| 论文题目: | High-throughput Cultivation and Identification of Bacteria from the Plant Root Microbiota |
| 英文论文题目: | High-throughput Cultivation and Identification of Bacteria from the Plant Root Microbiota |
| 第一作者: | Jingying Zhang, Yong-Xin Liu, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter, Paul Schulze-Lefert & Yang Bai |
| 英文第一作者: | Jingying Zhang, Yong-Xin Liu, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter, Paul Schulze-Lefert & Yang Bai |
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| 发表年度: | 2021-01-14 |
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| 摘要: | Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called ‘Culturome’ (https://github.com/YongxinLiu/Culturome) and a graphical user interface web server (http://bailab.genetics.ac.cn/culturome/). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8–9 weeks. |
| 英文摘要: | Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called ‘Culturome’ (https://github.com/YongxinLiu/Culturome) and a graphical user interface web server (http://bailab.genetics.ac.cn/culturome/). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8–9 weeks. |
| 刊物名称: | Nature Protocols |
| 英文刊物名称: | Nature Protocols |
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| 其它备注: | Jingying Zhang, Yong-Xin Liu, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter, Paul Schulze-Lefert & Yang Bai. High-throughput Cultivation and Identification of Bacteria from the Plant Root Microbiota. Nature Protocols. DOI:10.1038/s41596-020-00444-7 |
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