海岸带沉积物中氮循环功能微生物多样性

doi:10.3724/SP.J.1003.2013.12027

摘要/Abstract

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

Abstract

The coastal zone contains diverse habitats which are usually characterized by strong environmental 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 (Anammox) 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 reviewed. 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

龚骏, 宋延静, 张晓黎 (2013) 海岸带沉积物中氮循环功能微生物多样性. 生物多样性, 21, 433-444. DOI: 10.3724/SP.J.1003.2013.12027.

Jun Gong,Yanjing Song,Xiaoli Zhang (2013) Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments. Biodiversity Science, 21, 433-444. DOI: 10.3724/SP.J.1003.2013.12027.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2013.12027

https://www.biodiversity-science.net/CN/Y2013/V21/I4/433

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生境 Habitat	nifH分类(子类) nifH-based cluster (subcluster)	16S rRNA系统地位 Classification based on 16S rRNA gene	代表属 Representative genus	参考文献 Reference
潮间带微生物席/蓝细菌席Intertidal microbial/cyanobacterial mats	I (E) I (E) I (J) III (E) III (E)	Cyanobacteria γ-Proteobacteria α-Proteobacteria δ-Proteobacteria Fimicutes	Lyngbya Azotobacter Rhizobium Desulfovibrio Clostridium	Zehr et al., 1995 Steppe & Paerl, 2005
河口沉积物 Estuarine sediment	I (E) I (I) III (E) III (A)	γ-Proteobacteria γ-Proteobacteria δ-Proteobacteria Firmicutes	Azotobacter Klebsiella Desulfovibrio Clostridium	Burns et al., 2002 Herbert, 1999 Jones, 1982
盐沼植物根际 Rhizosphere in salt marsh	I (I) I (H) I (J) I (E) I (H) I (J) I (U)	γ-Proteobacteria γ-Proteobacteria α-Proteobacteria γ-Proteobacteria γ-Proteobacteria α-Proteobacteria γ-Proteobacteria	Enterobacter Spirilla Rhizobium Azotobacter Vibrio Azospirillum Psuedomonas	Bergholz et al., 2001 Lovell et al., 2001
海草(藻)根际 Rhizosphere of seagrass and seaweed	I (I) I (E) III (A) III (E)	γ-Proteobacteria γ-Proteobacteria Firmicutes δ-Proteobacteria	Rhizobium Azotobacter Clostridium Desulfomicrobium Desulfovibrio	Kirshtein et al., 1991 Smith et al., 2004 Achá et al., 2005
红树林根际 Rhizosphere of mangrove plants	I (I) I (E) III (A) I (J) I (I)	γ-Proteobacteria γ-Proteobacteria Firmicutes α-Proteobacteria γ-Proteobacteria	Rhizobium Azotobacter Clostridium Azospirillum Klebsiella	Thatoi et al., 2013
珊瑚礁区沉积物/珊瑚虫体 Sediment in coral reef environments/coral endosymbiot	I I (H) I (J) III (A)	Cyanobacteria γ-Proteobacteria α-Proteobacteria Firmicutes	Coccoid Vibrio Rhodobacter Clostridium	Olson et al., 2009 Rohwer et al., 2002

生境 Habitat	nifH分类(子类) nifH-based cluster (subcluster)	16S rRNA系统地位 Classification based on 16S rRNA gene	代表属 Representative genus	参考文献 Reference
潮间带微生物席/蓝细菌席Intertidal microbial/cyanobacterial mats	I (E) I (E) I (J) III (E) III (E)	Cyanobacteria γ-Proteobacteria α-Proteobacteria δ-Proteobacteria Fimicutes	Lyngbya Azotobacter Rhizobium Desulfovibrio Clostridium	Zehr et al., 1995 Steppe & Paerl, 2005
河口沉积物 Estuarine sediment	I (E) I (I) III (E) III (A)	γ-Proteobacteria γ-Proteobacteria δ-Proteobacteria Firmicutes	Azotobacter Klebsiella Desulfovibrio Clostridium	Burns et al., 2002 Herbert, 1999 Jones, 1982
盐沼植物根际 Rhizosphere in salt marsh	I (I) I (H) I (J) I (E) I (H) I (J) I (U)	γ-Proteobacteria γ-Proteobacteria α-Proteobacteria γ-Proteobacteria γ-Proteobacteria α-Proteobacteria γ-Proteobacteria	Enterobacter Spirilla Rhizobium Azotobacter Vibrio Azospirillum Psuedomonas	Bergholz et al., 2001 Lovell et al., 2001
海草(藻)根际 Rhizosphere of seagrass and seaweed	I (I) I (E) III (A) III (E)	γ-Proteobacteria γ-Proteobacteria Firmicutes δ-Proteobacteria	Rhizobium Azotobacter Clostridium Desulfomicrobium Desulfovibrio	Kirshtein et al., 1991 Smith et al., 2004 Achá et al., 2005
红树林根际 Rhizosphere of mangrove plants	I (I) I (E) III (A) I (J) I (I)	γ-Proteobacteria γ-Proteobacteria Firmicutes α-Proteobacteria γ-Proteobacteria	Rhizobium Azotobacter Clostridium Azospirillum Klebsiella	Thatoi et al., 2013
珊瑚礁区沉积物/珊瑚虫体 Sediment in coral reef environments/coral endosymbiot	I I (H) I (J) III (A)	Cyanobacteria γ-Proteobacteria α-Proteobacteria Firmicutes	Coccoid Vibrio Rhodobacter Clostridium	Olson et al., 2009 Rohwer et al., 2002

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