Biodiversity Science ›› 2013, Vol. 21 ›› Issue (4): 433-444.doi: 10.3724/SP.J.1003.2013.12027

Special Issue: Microbes Diversity

• Orginal Article • Previous Article     Next Article

Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments

Jun Gong1, *(), Yanjing Song1, 2, Xiaoli Zhang1   

  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
  • Received:2013-01-30 Accepted:2013-05-06 Online:2013-07-29
  • Gong Jun E-mail:jgong@yic.ac.cn

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

Table 1

Representatives of nitrogen-fixing microbes in different costal zone habitats (major phylogenetic groups based on 16S rRNA gene and subclusters based on nifH gene are shown)"

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
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