Candidatus Brocadia and Candidatus Kuenenia predominated in anammox bacterial community in selected Chinese paddy soils
Anammox bacteria have been widely investigated in both natural aquatic habitats and wastewater treatment reactors. However, their distribution in agricultural ecosystems which receive high reactive nitrogen input is hardly known. This study aims to examine the distribution and diversity of anammox bacteria in different Chinese paddy soils and along soil profile horizons.
Materials and methods
DNA was extracted from paddy soils which were collected from ten sites and along four soil depth horizons (0–20, 20–40, 40–60, 60–80 cm). Community structure and diversity of the anammox bacteria were analyzed using cloning and sequencing methods by targeting 16S ribosomal RNA (rRNA) genes. Quantitative PCR was conducted to study the abundance of anammox hzsB genes.
Results and discussion
Anammox bacterial 16S rRNA genes were not detected in most of the surface soil profile layers but present in all subsurface and deep horizons. Two genera, Candidatus Brocadia and Candidatus Kuenenia, were the only groups detected, and the former was predominant in tested soils. A site-specific distribution pattern of anammox bacteria and significant relationship between anammox bacteria community composition and soil pH and ammonium concentration were observed. The abundance of anammox bacteria hzsB gene ranged from 3.78 × 104 to 1.64 × 107 per gram of dry soil in all soils and significantly varied along the soil profile horizons.
Anammox bacteria were widely distributed in paddy soils, especially in subsurface and profile depth horizons. Candidatus Brocadia and Candidatus Kuenenia were the dominating anammox groups in the tested soils, and the two genera showed a site-specific distribution pattern across large Chinese paddy soil areas and along soil depth profiles.
KeywordsAnaerobic ammonium oxidation Anammox bacteria hzs gene Paddy soil
This work was financially supported by the National Science Foundation of China (41090281, 41025004, 41322007). We would like to thank Prof. Wenxue Wei and Ms. Yijun Zhu for their assistance in soil sampling and Drs. Peng Cao and Yu Dai for their help in soil physiochemical analysis.
- Chen H, Liu S, Yang F, Xue Y, Wang T (2009) The development of simultaneous partial nitrification, ANAMMOX and denitrification (SNAD) process in a single reactor for nitrogen removal. Bioresour Technol 100:1548–1554Google Scholar
- Dong LF, Smith CJ, Papaspyrou S, Stott A, Osborn AM, Nedwell DB (2009) Changes in benthic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne estuary, United Kingdom). Appl Environ Microbiol 75:3171–3179CrossRefGoogle Scholar
- Hou L, Zheng Y, Liu M, Gong J, Zhang X, Yin G, You L (2013) Anaerobic ammonium oxidation (anammox) bacterial diversity, abundance, and activity in marsh sediments of the Yangtze Estuary. J Geophys Res 118:1237–1246Google Scholar
- Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ (2009) Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol 44:65–84Google Scholar
- Li M, Gu JD (2013) Community structure and transcript responses of anammox bacteria, AOA, and AOB in mangrove sediment microcosms amended with ammonium and nitrite. Appl Microbiol Biotechnol 97:9859–9874Google Scholar
- Schmid M, Twachtmann U, Klein M, Strous M, Juretschko S, Jetten M, Metzger JW, Schleifer KH, Wagner, M (2000) Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Systematic and Applied Microbiology 23:93–106Google Scholar
- Schmid MC, Maas B, Dapena A, van de Pas-Schoonen K, van de Vossenberg J, Kartal B, van Niftrik L, Schmidt I, Cirpus I, Kuenen JG, Wagner M, Sinninghe Damste JS, Kuypers M, Revsbech NP, Mendez R, Jetten MS, Strous M (2005) Biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria. Appl Environ Microbiol 71:1677–1684Google Scholar
- Schmid MC, Risgaard-Petersen N, van de Vossenberg J, Kuypers MM, Lavik G, Petersen J, Hulth S, Thamdrup B, Canfield D, Dalsgaard T, Rysgaard S, Sejr MK, Strous M, den Camp HJ, Jetten MS (2007) Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity. Environ Microbiol 9:1476–1484Google Scholar
- Schmid M, Schmitz-Esser S, Jetten M, Wagner M (2011) 16S‐23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium‐oxidizing bacteria: implications for phylogeny and in situ detection. Environ Microbiol 3:450–459Google Scholar
- Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10:1601–1611Google Scholar
- Shen LD, Liu S, Lou LP, Liu WP, Xu XY, Zheng P, Hu BL (2013) Broad distribution of diverse anaerobic ammonium-oxidizing bacteria in Chinese agricultural soils. Appl Environ Microbiol 79:6167–6172Google Scholar
- Wang Y, Zhu G, Harhangi HR, Zhu B, Jetten MS, Yin C, Op den Camp HJ (2012a) Co-occurrence and distribution of nitrite-dependent anaerobic ammonium and methane-oxidizing bacteria in a paddy soil. FEMS Microbiol Lett 336:79–88Google Scholar
- Wang S, Zhu G, Peng Y, Jetten MS, and Yin C (2012b) Anammox bacterial abundance, activity, and contribution in riparian sediments of the Pearl River estuary. Environ Sci Technol 46:8834–8842Google Scholar
- Wang J, Gu JD (2013) Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China. Appl Microbiol Biotechnol 97:1785–1798Google Scholar
- Wang TF, Gu JD (2014) Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms. Appl Microbiol Biotechnol 98:3257–3274Google Scholar
- Yamamoto T, Takaki K, Koyama T, Furukawa K (2008) Long-term stability of partial nitritation of swine wastewater digester liquor and its subsequent treatment by Anammox. Bior Tech 99(14):6419–6425Google Scholar
- Zhu ZL, Chen DL (2002) Nitrogen fertilizer use in China—contributions to food production, impacts on the environment and best management strategies. Nutr Cycl Agroecosys 63:117–127Google Scholar
- Zhu G, Wang S, Feng X, Fan G, Jetten MS, Yin C (2011) Anammox bacterial abundance, biodiversity and activity in a constructed wetland. Environ Sci Technol 45:9951–9958Google Scholar