硝化微生物富集及其种群结构与基因表达分析

doi:10.3969/j.issn.1000-5641.2019.03.018

华东师范大学学报(自然科学版) ›› 2019, Vol. 2019 ›› Issue (3): 164-173.doi: 10.3969/j.issn.1000-5641.2019.03.018

硝化微生物富集及其种群结构与基因表达分析

余晨笛¹, 侯立军¹, 郑艳玲^2,3, 刘敏^2,3, 尹国宇^2,3, 高娟¹, 刘程¹, 常永凯¹

1. 华东师范大学河口海岸学国家重点实验室, 上海 200241;
2. 华东师范大学地理信息科学教育部重点实验室, 上海 200241;
3. 华东师范大学地理科学学院, 上海 200241

收稿日期:2018-03-02 出版日期:2019-05-25 发布日期:2019-05-30
通讯作者: 侯立军,男,博士生导师,教授,研究方向为河口海岸生源要素循环.E-mail:ljhou@sklec.ecnu.edu.cn. E-mail:ljhou@sklec.ecnu.edu.cn
作者简介:余晨笛,女,硕士研究生,研究方向为河口海岸生源要素循环.E-mail:fish5691@qq.com.
基金资助:
国家重点研发计划课题（2016YFA0600904）；国家自然科学基金（41725002，41671463，41130525，41322002，41601530）

Community structure and gene expression analysis for nitrifier enrichment cultures

YU Chen-di¹, HOU Li-jun¹, ZHENG Yan-ling^2,3, LIU Min^2,3, YIN Guo-yu^2,3, GAO Juan¹, LIU Cheng¹, CHANG Yong-kai¹

1. State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China;
2. Key Laboratory of Geographic Information Science(Ministry of Education), East China Normal University, Shanghai 200241, China;
3. School of Geographic Sciences, East China Normal University, Shanghai 200241, China

Received:2018-03-02 Online:2019-05-25 Published:2019-05-30

摘要/Abstract

摘要： 对采集的长江口潮滩沉积物进行了硝化微生物的富集培养，通过宏基因组技术分析了富集物中硝化微生物的种群结构.检测到4类硝化微生物（占测序总reads的34.7%），包括新近发现的全程氨氧化微生物（complete ammonia oxidizers，comammox）、严格的亚硝酸盐氧化菌Nitrospira、β-变形菌门氨氧化细菌及氨氧化古菌.其中，comammox占硝化微生物类群的48%.此外，基于宏转录组技术分析了4类硝化菌群的基因表达特征（依据Evolutionarygenealogy of genes：Non-supervised Orthologous Groups数据库）.研究探讨了潮滩沉积物富集物中硝化微生物的种群结构与基因表达特征，证明了长江口潮滩沉积环境中comammox的存在，并验证了其基因表达活性.研究结果加深了对河口地区硝化微生物的认识，对于未来硝化过程的分子生态学研究有重要启示意义.

关键词: 硝化微生物, 富集培养, 潮滩沉积物, 种群丰度, 基因表达

Abstract: Nitrifiers were enriched from the tidal sediments of the Yangtze Estuary. Four kinds of nitrifying groups (accounting for 34.7% of the total reads) were detected based on metagenomics, including the recently discovered complete ammonia oxidizers (comammox), strictly nitrite-oxidizing Nitrospira, β-proteobacterial ammonia-oxidizing bacteria, and ammonia-oxidizing archaea. Comammox accounted for 48% of the detected nitrifiers. In addition, gene expression patterns of the nitrifier group (according to the classification in Evolutionary genealogy of genes:Non-supervised Orthologous Groupsdatabase) were analyzed based on metatranscriptomics. The present study showed the community structure and gene expression characteristics of nitrifiers enriched from the tidal sediments, especially the newly discovered comammox. Results enriched our knowledge about the nitrifying communities of estuarine environment, which have great significance to the further molecular ecology research of the nitrification processes.

Key words: nitrifier, enrichment culture, tidal sediment, community structure, gene expression

中图分类号:

X172

余晨笛, 侯立军, 郑艳玲, 刘敏, 尹国宇, 高娟, 刘程, 常永凯. 硝化微生物富集及其种群结构与基因表达分析[J]. 华东师范大学学报(自然科学版), 2019, 2019(3): 164-173.

YU Chen-di, HOU Li-jun, ZHENG Yan-ling, LIU Min, YIN Guo-yu, GAO Juan, LIU Cheng, CHANG Yong-kai. Community structure and gene expression analysis for nitrifier enrichment cultures[J]. Journal of East China Normal University(Natural Sc, 2019, 2019(3): 164-173.

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硝化微生物富集及其种群结构与基因表达分析

Community structure and gene expression analysis for nitrifier enrichment cultures

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