Biodiv Sci ›› 2013, Vol. 21 ›› Issue (4): 433-444.DOI: 10.3724/SP.J.1003.2013.12027

Special Issue: 微生物多样性专辑

• Orginal Article • Previous Articles     Next Articles

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:2013-07-20 Published:2013-07-29
  • Contact: Gong Jun

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