| ZHAO Wei,WANG Jingjing,LIANG Yajie,HUANG Zhiyong. 2017. Development of a 16S rRNA gene-based microarray for the detection of marine bacterioplankton community. Acta Oceanologica Sinica, 36(10):106－114 |
| Development of a 16S rRNA gene-based microarray for the detection of marine bacterioplankton community |
| 一种基于16S rRNA基因检测海洋浮游细菌群落的微阵列基因芯片 |
| Received:April 26, 2016 |
| DOI：10.1007/s13131-017-1055-6 |
| Key words:microarray bacterioplankton community 16S rRNA gene marine environment |
| 中文关键词: 微阵列芯片 浮游细菌群落 16S rRNA基因 海洋环境 |
| 基金项目: |
| Author Name | Affiliation | E-mail | | ZHAO Wei | Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China | | | WANG Jingjing | Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China | | | LIANG Yajie | Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China | | | HUANG Zhiyong | Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China | huang_zy@tib.cas.cn |
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| Abstract: |
| A better understanding of bacterioplankton community shifts following change in marine environments is critical to predict the marine ecosystem function. In order to get a snapshot of the microbial taxonomy profiling of a wide range marine area, a quick, convenient and low cost method would be favorable. In this study, we developed a 16S rRNA gene-based microarray using ARB software, which contained 447 probes targeting 160 families of marine bacteria. The specificity, sensitivity and quantitative capability of this microarray were assessed by single cloned 16S rRNA genes. The reliability of this microarray was tested by eight environmental samples. The results showed that the microarray was specific, only 1.16% false results were detected in five single-clone hybridization tests. The microarray could detect DNA samples as few as 1 ng/μL and the signal intensity could reflect the relative abundance of the bacteria in the range of 1 ng/μL to 100 ng/μL of DNA concentration. Hybridization with environmental samples showed that it can discriminate bacterioplankton communities by sites and time. High throughput sequencing results from the eight samples confirmed the hybridization results. It indicated that this developed microarray could be used as a convenient tool to monitor the bacterioplankton community in marine environment. |
| 中文摘要: |
| 浮游细菌群落结构的变化对于指示海洋环境、预测海洋系统生态功能至关重要。为满足对微生物种群进行全面了解和检测的要求，亟需一种简单、快速、高效经济的检测手段。本研究基于16S rRNA基因，利用ARB软件设计并构建了一套微阵列基因芯片，包含447种探针，能够检测160个海洋细菌科。使用单克隆16S rRNA基因检测芯片的杂交特异性、检测灵敏度以及定量能力，利用来自中国东海的8个海水样品进行芯片检测可靠性的验证。单克隆与芯片杂交结果显示了1.16%的杂交错配率；梯度稀释DNA样品的检测结果显示，芯片能够检测到不低于1 ng/μL的样品，同时，杂交信号随DNA浓度（1 ng/μL到100 ng/μL）的增加呈线性增强。对环境样品的杂交结果显示，芯片能将不同来源的微生物群落进行区分，并且与高通量测序检测结果一致。说明该研究中的微阵列芯片是一种简便有效的监测海洋浮游细菌群落的工具。 |
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