海岸带沉积物中氮循环功能微生物多样性

生物多样性 2013, 21 (4): 433–444 Doi: 10.3724/SP.J.1003.2013.12027 Biodiversity Science http: //

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收稿日期: 2013-01-30; 接受日期: 2013-05-06

基金项目: 中科院重要方向性项目(No. KZCX2-YW-JC203; KSCX2-EW-G-12B)、国家自然科学基金项目(No. 41206155)和山东省自然科学杰出青年基金(JQ201210) ∗

通讯作者 Author for correspondence. E-mail: jgong@

海岸带沉积物中氮循环功能微生物多样性

龚 骏1* 宋延静1,2 张晓黎1

1 (中国科学院烟台海岸带研究所微生物生态与物质循环实验室, 山东烟台 264003)

2 (中国科学院大学, 北京 100049)

摘要: 海岸带生境类型多样, 环境梯度明显, 是研究微生物多样性、群落结构与功能关系及调控机制的天然实验场。沉积物是海岸带环境中营养盐再生与转化发生的重要场所, 其中多种微生物类群在氮素循环过程中扮演重要角色。本文重点介绍海岸带沉积物中固氮菌、氨氧化菌、厌氧氨氧化菌、反硝化与硝酸盐铵化微生物的基于16S rRNA 基因的物种多样性和基于关键酶基因nifH 、amoA 、narG 、nirS 、nirK 、nosZ 、nrfA 、hzo 、hzs 等的功能多样性; 总结了在海岸带特有生境(如河口、潮间带、海草藻床、红树林、盐沼、珊瑚礁、浅海等)及污染胁迫、生物扰动等条件下各功能类群的群落组成特征及时空变化规律, 并提出今后需要重点关注新的培养技术和方法的开发, 以进一步提高微生物的可培养性, 将单细胞基因组测序与分析技术、DNA 和RNA 结合起来研究, 以全面了解氮循环微生物多样性、参与介导硝酸盐铵化过程的微生物多样性等方面。

关键词: 分子生态, 功能基因多样性, 海洋底栖生物, 群落组成, 物种多样性, 系统分类

Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments

Jun Gong 1*, Yanjing Song 1,2, Xiaoli Zhang 1

1 Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003

2 University of Chinese Academy of Sciences, Beijing 100049

Abstract: The coastal zone contains diverse habitats which are usually characterized by strong environ-mental gradients (e.g. salinity, nutrients and pollutants). This makes the coastal zone an ideal experimental laboratory for describing microbial diversity and testing hypotheses on community structure, function and control. Coastal sediment is of significance in nutrient regeneration and transformation involving different assemblages of microbes in the nitrogen cycle. This review focuses on 16S rRNA gene-based phylogenetic diversity and the key enzyme encoding gene-based (e.g. nifH , amoA , narG , nirS , nirK , nosZ , nrfA , hzo and hzs ) functional diversity of nitrogen fixing, ammonia oxidizing and anaerobic ammonia oxidation (Anam-mox) bacteria as well as bacteria and fungi involved in denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Characteristics of community composition and diversity of nitrogen cycling microbes in different habitats (e.g. estuarine, intertidal flats, seagrass or seaweed beds, mangroves, salt marsh, coral reefs, and shallow seas), and their spatiotemporal patterns under benthic pollution or bioturbation are re-viewed. Future directions for a better understanding diversity of nitrogen cycling microbes are suggested, such as culture methods and technologies, and single-cell sequencing, etc.

Key words: community composition, functional genes, functional diversity, marine benthos, molecular ecology, phylogenetic diversity, phylogenetic classification

生物多样性对生态系统功能与服务至关重要(Cardinale, 2011; Midgley, 2012), 物种共存机制在

多样性与生态系统功能关系的形成中扮演着重要角色(张全国和张大勇, 2003)。微生物在全球生物地