Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

doi:10.1016/S2095-3119(13)60426-8

Journal of Integrative Agriculture ›› 2014, Vol. 13 ›› Issue (4): 870-880.DOI: 10.1016/S2095-3119(13)60426-8

Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

SONG Ya-na , LIN Zhi-min

Institute of Biological Technology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, P.R.China

收稿日期:2012-11-12 出版日期:2014-04-01 发布日期:2014-04-16
通讯作者: SONG Ya-na, Mobile: 15980168116, Fax: +86-591-87826470, E-mail: syana@sina.com
作者简介:SONG Ya-na, Mobile: 15980168116, Fax: +86-591-87826470, E-mail: syana@sina.com
基金资助:
The study was supported by the National Natural Science Foundation of China (40801097) and the Natural Science Foundation of Fujian Province, China (2012J01107).

Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

SONG Ya-na , LIN Zhi-min

Institute of Biological Technology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, P.R.China

Received:2012-11-12 Online:2014-04-01 Published:2014-04-16
Contact: SONG Ya-na, Mobile: 15980168116, Fax: +86-591-87826470, E-mail: syana@sina.com
About author:SONG Ya-na, Mobile: 15980168116, Fax: +86-591-87826470, E-mail: syana@sina.com
Supported by:
The study was supported by the National Natural Science Foundation of China (40801097) and the Natural Science Foundation of Fujian Province, China (2012J01107).

摘要/Abstract

摘要： Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). However, the relative importance of AOB and AOA to nitrification in terrestrial ecosystems is not well understood. The aim of this study was to investigate the effect of the nitrogen input amount on abundance and community composition of AOB and AOA in red paddy soil. Soil samples of 10-20 cm (root layer soil) and 0-5 cm (surface soil) depths were taken from a red paddy. Rice in the paddy was fertilized with different rates of N as urea of N1 (75 kg N ha-1 yr-1), N2 (150 kg N ha-1 yr-1), N3 (225 kg N ha-1 yr-1) and CK (without fertilizers) in 2009, 2010 and 2011. Abundance and community composition of ammonia oxidizers was analyzed by real-time PCR and denaturing gradient gel electrophoresis (DGGE) based on amoA (the unit A of ammonia monooxygenase) gene. Archaeal amoA copies in N3 and N2 were significantly (P<0.05) higher than those in CK and N1 in root layer soil or in surface soil under tillering and heading stages of rice, while the enhancement in bacterial amoA gene copies with increasing of N fertilizer rates only took on in root layer soil. N availability and soil NO3 --N content increased but soil NH4 +-N content didn’t change with increasing of N fertilizer rates. Otherwise, the copy numbers of archaeal amoA gene were higher (P<0.05) than those of bacterial amoA gene in root lary soil or in surface soil. Redundancy discriminate analysis based on DGGE bands showed that there were no obvious differs in composition of AOA or AOB communities in the field among different N fertilizer rates. Results of this study suggested that the abundance of ammonia-oxidizers had active response to N fertilizer rates and the response of AOA was more obvious than that of AOB. Similarity in the community composition of AOA or AOB among different N fertilizer rates indicate that the community composition of ammonia-oxidizers was relatively stable in the paddy soil at least in short term for three years.

关键词: ammonia-oxidizing bacteria , ammonia-oxidizing archaea , nitrogen fertilizer rates , paddy soil

Abstract: Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). However, the relative importance of AOB and AOA to nitrification in terrestrial ecosystems is not well understood. The aim of this study was to investigate the effect of the nitrogen input amount on abundance and community composition of AOB and AOA in red paddy soil. Soil samples of 10-20 cm (root layer soil) and 0-5 cm (surface soil) depths were taken from a red paddy. Rice in the paddy was fertilized with different rates of N as urea of N1 (75 kg N ha-1 yr-1), N2 (150 kg N ha-1 yr-1), N3 (225 kg N ha-1 yr-1) and CK (without fertilizers) in 2009, 2010 and 2011. Abundance and community composition of ammonia oxidizers was analyzed by real-time PCR and denaturing gradient gel electrophoresis (DGGE) based on amoA (the unit A of ammonia monooxygenase) gene. Archaeal amoA copies in N3 and N2 were significantly (P<0.05) higher than those in CK and N1 in root layer soil or in surface soil under tillering and heading stages of rice, while the enhancement in bacterial amoA gene copies with increasing of N fertilizer rates only took on in root layer soil. N availability and soil NO3 --N content increased but soil NH4 +-N content didn’t change with increasing of N fertilizer rates. Otherwise, the copy numbers of archaeal amoA gene were higher (P<0.05) than those of bacterial amoA gene in root lary soil or in surface soil. Redundancy discriminate analysis based on DGGE bands showed that there were no obvious differs in composition of AOA or AOB communities in the field among different N fertilizer rates. Results of this study suggested that the abundance of ammonia-oxidizers had active response to N fertilizer rates and the response of AOA was more obvious than that of AOB. Similarity in the community composition of AOA or AOB among different N fertilizer rates indicate that the community composition of ammonia-oxidizers was relatively stable in the paddy soil at least in short term for three years.

Key words: ammonia-oxidizing bacteria , ammonia-oxidizing archaea , nitrogen fertilizer rates , paddy soil

SONG Ya-na , LIN Zhi-min. Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates[J]. Journal of Integrative Agriculture, 2014, 13(4): 870-880.

参考文献

Alvey S, Yang C H, Bürkert A, Crowley D E. 2003. Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils. Biology and Fertility of Soils, 37, 73-82

Avrahami S, Conrad R. 2003. Patterns of community change among ammonia oxidizers in meadow soils upon long- term incubation at different temperatures. Applied and Environmental Microbiology, 69, 6152-6164

Bao S D. 2007. Soil Analysis in Agricultural Chemistry. China Agricultural Press, Beijing. pp. 30-34, 56-58, 81- 83, 106-108 (in Chinese)

Bowatte S, Jia Z, Ishihara R, Nakajima Y, Asakawa S, Kimura M. 2006. Molecular analysis of the ammonia- oxidizing bacterial community in the surface soil layer of a Japanese paddy field. Soil Science and Plant Nutrition, 52, 427-431

Brune A, Frenzel P, Cypionka H. 2000. Life at the oxic- anoxic interface: Microbial activities and adaptations. FEMS Microbiology Reviews, 24, 691-710

Bruns M A, Stephen J R, Kowalchuk G A, Prosser J I, Paul E A. 1999. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Applied and Environmental Microbiology, 65, 2994-3000

Cassman K G, Kropff M J, Gaunt J, Peng S. 1993. Nitrogen use efficiency of rice reconsidered: What are the key constraints? Plant and Soil, 155/156, 359-362

Chen X P, Zhu Y G, Xia Y, Shen J P, He J Z. 2008. Ammonia-oxidizing archeae: Important players in paddy rhizosphere soil? Environmental Microbiology, 10, 1978-1987

Di H J, Cameron K C, Shen J P, Winefield C S, O’Callaghan M, Bowatte S, He J Z. 2009. Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nature Geoscience, 2, 621-624

Di H J, Cameron K C, Shen J P, Winefield C S, O’Callaghan M, Bowatte S, He J Z. 2010. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiology Ecology, 72, 386-394

Erguder T H, Boon N, Wittebolle L, Marzorati M, Verstraete W. 2009. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiology Reviews, 33, 855-869

Francis C A, Roberts K J, Beman J M, Santoro A E, Oakley B B. 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America, 102, 14683-14688

Gubry-Rangin C, Nicol G W, Posser J I. 2010. Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiology Ecology, 74, 566-574

He J Z, Shen J P, Zhang L M, Zhu Y G, Zheng Y M, Xu M G, Di H J. 2007. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinses upland red soil under long-term fertilization practices. Environmental Microbiology, 9, 2364-2374

Jia Z J, Conrad R. 2009. Bacteria rather than archeae dominate microbial ammonia oxidation in an agricultural soil. Environmental Microbiology, 11, 1685-1671

Kronzucker H J, Siddiqi M Y, Glass M A D, Kirk G J D. 2000. Comparative kinetic analysis of ammonium and nitrate acquisition by tropical lowland rice: Implications for rice cultivation and yield potential. New Phytologist, 145, 471-476

Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol G W, Prosser J I, Schuster S C, Schleper C. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soil. Nature, 442, 806-809

Lu L, Han W Y, Zhang J B, Wu Y C, Wang B Z, Lin X G, Zhu J G, Cai Z C, Jia Z J. 2012. Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea. The International Society for Microbial Ecology Journal, 6, 1978-1984

Marschner P, Neumann G, Kania A, Weiskopf L, Lieberei R. 2002. Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.). Plant and Soil, 246, 167-174

Muyzer G, Waal de E C, Uitterlinden A G. 1993. Profiling of complex microbial population by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695-700

Nicol G W, Leininger S, Schleper C, Prosser J I. 2008. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology, 10, 2966- 2978.

Phillips C J, Harris D, Dollhopf S L, Gross K L, Prosser J I, Paul E A. 2000. Effects of agronomic treatments on structure and function of ammonia-oxidizing communities. Applied and Environmental Microbiology, 66, 5410-5418

Prosser J I, Embley T M. 2002. Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Antonie van Leeuwenhoek, 81, 165-179

Robertson G P. 1982. Factors regulating nitrification in primary and secondary succession. Ecology, 63, 1561- 1573.

Rotthauwe J H, Witzel K P, Liesack W. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology, 63, 4704-4712

Schleper C, Jurgens G, onuscheit M. 2005. Genomic studies of uncultivated archaea. Nature Reviews Microbiology, 3, 479-488

Shen J P, Zhang L M, Zhu Y G, Zhang J B, He J Z. 2008. Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environmental Microbiology, 10, 1601-1611

Song Y N, Lin Z M. 2010. Changes in community structures of ammonia-oxidizers and potential nitrification rates in paddy soilat different growth stages of rice. Acta Pedologica Sinica, 47, 168-175 (in Chinese)

Stephen J R, McCaig A E, Smith Z, Prosser J I, Embley T M. 1996. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Applied and Environmental Microbiology, 62, 4147-4154

Treusch A H, Leininger S, Kletzin A, Schuster S C, Klenk H P, Schleper C. 2005. Novel genes for nitrite reductase and amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology, 7, 1985-1995

Wang M Y, Siddiqi M Y, Ruth T J, Glass A D M. 1993. Ammonium uptake by rice roots. I. Fluxes and subcellular distribution of 13NH4+. Plant Physiology, 103, 1249-1258

Woese C R, Weisburg W G, Hahn C M, Paster B J, Zablen L B, Lewis B J, Mackie T J, Ludwig W, Stackebrandt E. 1985. The phylogeny of the purple bacteria: The gamma subdivision. Systematic and Applied Microbiology, 6, 25-33

Wuchter C, Abbas B, Coolen M J L, Herfort L, Bleijswijk van J, Timmers P, Strous M, Teira E, Herndl G J, Middelburg J J, et al. 2006. Archaeal nitrification in the ocean. Proceedings of the National Academy of Sciences of the United States of America, 103, 12317-12322

Ying J Y, Zhang L M, He J Z. 2010. Putative ammonia- oxidizing bacteria and archaea in an acid red soil with different land utilization patterns. Environmental Microbiology Reports, 2, 302-312

[1]	CHEN Zhong-du, ZHANG Hai-lin, S Batsile Dikgwatlhe, XUE Jian-fu, QIU Kang-cheng, TANG Hai-ming, CHEN fu. Soil carbon storage and stratification under different tillage/ residue-management practices in double rice cropping system[J]. Journal of Integrative Agriculture, 2015, 14(8): 1551-1560.
[2]	YANG Zeng-ping, ZHENG Sheng-xian, NIE Jun, LIAO Yu-lin, XIE Jian. Effects of Long-Term Winter Planted Green Manure on Distribution and Storage of Organic Carbon and Nitrogen in Water-Stable Aggregates of Reddish Paddy Soil Under a Double-Rice Cropping System[J]. Journal of Integrative Agriculture, 2014, 13(8): 1772-1781.
[3]	HUANG Qing-hai, LI Da-ming, LIU Kai-lou, YU Xi-chu, YE Hui-cai, HU Hui-wen, XU Xiao-lin. Effects of Long-Term Organic Amendments on Soil Organic Carbon in a Paddy Field: A Case Study on Red Soil[J]. Journal of Integrative Agriculture, 2014, 13(3): 570-576.
[4]	LIU Ling-zhi, QIN Si-jun, Lü De-guo, WANG Bing-ying , YANG Ze-yuan. Variation of Potential Nitrification and Ammonia-Oxidizing Bacterial Community with Plant-Growing Period in Apple Orchard Soil[J]. Journal of Integrative Agriculture, 2014, 13(2): 415-425.
[5]	LIU Zhan-jun, ZHOU Wei, SHEN Jian-bo, LI Shu-tian, LIANG Guo-qing, WANG Xiu-bin, SUN Jing-wen , AI Chao. Soil Quality Assessment of Acid Sulfate Paddy Soils with Different Productivities in Guangdong Province, China[J]. Journal of Integrative Agriculture, 2014, 13(1): 177-186.
[6]	LIAO Yu-lin, ZHENG Sheng-xian, NIE Jun, XIE Jian, LU Yan-hong , QIN Xiao-bo. Long-Term Effect of Fertilizer and Rice Straw on Mineral Composition and Potassium Adsorption in a Reddish Paddy Soil[J]. Journal of Integrative Agriculture, 2013, 12(4): 694-710.
[7]	YANG Zeng-ping, XU Ming-gang, ZHENG Sheng-xian, NIE Jun, GAO Ju-sheng, LIAO Yu-lin , XIE Jian . Effects of Long-Term Winter Planted Green Manure on Physical Properties of Reddish Paddy Soil Under a Double-Rice Cropping System[J]. Journal of Integrative Agriculture, 2012, 12(4): 655-664.
[8]	HAO Rui-jun, LI Zhong-pei, CHE Yu-ping. Differences in Organic C Mineralization Between Aerobic and SubmergedConditions in Paddy Soils of Southern Jiangsu Province, China[J]. Journal of Integrative Agriculture, 2011, 10(9): 1410-1418.
[9]	LIU Ming, Klemens Ekschmitt, ZHANG Bin, Stephanie I J Holzhauer, LI Zhong-pei, ZHANG Tao-lin , Sabine Rauch . Effect of Intensive Inorganic Fertilizer Application on Microbial Properties in a Paddy Soil of Subtropical China[J]. Journal of Integrative Agriculture, 2011, 10(11): 1758-1764.

Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 9

编辑推荐

Metrics