Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments

doi:10.3724/SP.J.1003.2013.12027

Abstract

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

Jun Gong,Yanjing Song,Xiaoli Zhang. Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments[J]. Biodiv Sci, 2013, 21(4): 433-444.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2013.12027

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

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References 113

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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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