Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments
- 1.2k Downloads
Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 104–6.47 × 105 copies g−1 sediment) was always greater than that of AOA amoA gene (7.98 × 103–3.51 × 105 copies g−1 sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03–5.39 pmol N copy−1 day−1) compared with winter (0.16–0.38 pmol N copy−1 day−1), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons.
KeywordsNitrification Ammonia-oxidizing bacteria (AOB) Ammonia-oxidizing archaea (AOA) amoA gene Intertidal sediment Yangtze estuary
This work was funded by the National Natural Science Foundations (Nos. 41130525, 40721004, 41021064, and 41071135) and the State Key Laboratory of Estuarine and Coastal Research (No. 2010RCDW07). It was also supported by the Fundamental Research Funds for the Central Universities and the Marine Scientific Research Project for Public Interest (No. 200905007). We thank Drs. Xiaoli Zhang, Jun Gong and Bing Xie for sharing their analytical expertise on measurements of ammonia-oxidizers. Professor Wayne S. Gardner and the anonymous reviewers are thanked for their constructive comments on a preliminary draft of the manuscript.
- Beman JM, Popp BN, Francis CA (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J 2:429–441Google Scholar
- Bernhard AE, Landry ZC, Blevins A, de la Torre JR, Giblin AE, Stahl DA (2010) Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates. Appl Environ Microbiol 77:2026–2034Google Scholar
- Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G (2008) Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. Microbiology 154:2084–2095Google Scholar
- Dang H, Li J, Chen R, Wang L, Guo L, Zhang Z, Klotz MG (2010) Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China. Appl Environ Microbiol 76:4691–4702Google Scholar
- Fan GN, Zhu GB, Wang Y, Wang SY, Wang CX, Yin CQ (2010) New functional microorganisms in nitrogen cycle restoration of river riparian ecosystems. Acta Scientiae Circumstantiae 30:1558–1563Google Scholar
- Hatzenpichler R, Lebedeva EV, Spieck E, Stoecher K, Richter A, Daims H, Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci 105:134–2139Google Scholar
- Henriksen K, Kemp WM (1986) Nitrification in estuarine and coastal marine sediments: Methods, patterns and regulating factors, p 207–250. In: Blackburn TH, Sørensen J (eds) Nitrogen cycling in coastal marine environments. Wiley, New YorkGoogle Scholar
- Hou LJ, Liu M, Xu SY, Ou DN, Yu J, Cheng SB, Lin X, Yang Y (2007) The effects of semi-lunar spring and neap tidal change on nitrification, denitrification, and N2O vertical distribution in the intertidal sediments of the Yangtze estuary, China. Estuar Coast Shelf Sci 73:607–616CrossRefGoogle Scholar
- Mußmann M, Brito I, Pitcher A, Sinninghe Damsté JS, Hatzenpichler R, Richter A, Nielsen JL, Halkjær Nielsen P, Müller A, Daims H, Wagner M, Head IM (2011) Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc Natl Acad Sci 108:16771–16776Google Scholar
- Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66:5368–5382PubMedCrossRefGoogle Scholar
- Vitousek PM, Aber JD, Howarth RW, Likens GE, Matson PA, Schindler DW (1997) Technical report: human alteration of the global nitrogen cycle: sources and consequences. Ecol Appl 7:737–750Google Scholar