|
|
|
|
|
| Impact of Long-Term Fertilization on Community Structure of Ammonia Oxidizing and Denitrifying Bacteria Based on amoA and nirK Genes in a Rice Paddy from Tai Lake Region, China |
| JIN Zhen-jiang, LI Lian-qing, LIU Xiao-yu, PAN Gen-xing, Qaiser Hussein , LIU Yong-zhuo |
1、Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R.China
2、Guilin University of Technology, Guilin 541004, P.R.China |
|
|
|
摘要 Ammonia oxidizing (AOB) and denitrifying bacteria (DNB) play an important role in soil nitrogen transformation in natural and agricultural ecosystems. Effects of long-term fertilization on abundance and community composition of AOB and DNB were studied with targeting ammonia monooxygenase (amoA) and nitrite reductase (nirK) genes using polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR, respectively. A field trial with different fertilization treatments in a rice paddy from Tai Lake region, centre East China was used in this study, including no fertilizer application (NF), balanced chemical fertilizers (CF), combined organic/inorganic fertilizer of balanced chemical fertilizers plus pig manure (CFM), and plus rice straw return (CFS). The abundances and richnesses of amoA and nirK were increased in CF, CFM and CFS compared to NF. Principle component analysis of DGGE profiles showed significant difference in nirK and amoA genes composition between organic amended (CFS and CFM) and the non-organic amended (CF and NF) plots. Number of amoA copies was significantly positively correlated with normalized soil nutrient richness (NSNR) of soil organic carbon (SOC) and total nitrogen (T-N), and that of nirK copies was with NSNR of SOC, T-N plus total phosphorus. Moreover, nitrification potential showed a positive correlation with SOC content, while a significantly lower denitrification potential was found under CFM compared to under CFS. Therefore, SOC accumulation accompanied with soil nutrient richness under long-term balanced and organic/inorganic combined fertilization promoted abundance and diversity of AOB and DNB in the rice paddy.
Abstract Ammonia oxidizing (AOB) and denitrifying bacteria (DNB) play an important role in soil nitrogen transformation in natural and agricultural ecosystems. Effects of long-term fertilization on abundance and community composition of AOB and DNB were studied with targeting ammonia monooxygenase (amoA) and nitrite reductase (nirK) genes using polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR, respectively. A field trial with different fertilization treatments in a rice paddy from Tai Lake region, centre East China was used in this study, including no fertilizer application (NF), balanced chemical fertilizers (CF), combined organic/inorganic fertilizer of balanced chemical fertilizers plus pig manure (CFM), and plus rice straw return (CFS). The abundances and richnesses of amoA and nirK were increased in CF, CFM and CFS compared to NF. Principle component analysis of DGGE profiles showed significant difference in nirK and amoA genes composition between organic amended (CFS and CFM) and the non-organic amended (CF and NF) plots. Number of amoA copies was significantly positively correlated with normalized soil nutrient richness (NSNR) of soil organic carbon (SOC) and total nitrogen (T-N), and that of nirK copies was with NSNR of SOC, T-N plus total phosphorus. Moreover, nitrification potential showed a positive correlation with SOC content, while a significantly lower denitrification potential was found under CFM compared to under CFS. Therefore, SOC accumulation accompanied with soil nutrient richness under long-term balanced and organic/inorganic combined fertilization promoted abundance and diversity of AOB and DNB in the rice paddy.
|
|
Received: 25 December 2013
Accepted:
|
| Fund: This work was supported by the National Natural Science Foundation of China (40830528 and 40710019002). |
|
Corresponding Authors:
PAN Gen-xing, Tel: +86-25-84398657, E-mail: pangenxing@aliyun.com
E-mail: pangenxing@aliyun.com
|
| About author: JIN Zhen-jiang, E-mail: zhenjiangjinjin@163.com |
Cite this article:
JIN Zhen-jiang, LI Lian-qing, LIU Xiao-yu, PAN Gen-xing, Qaiser Hussein , LIU Yong-zhuo.
2014.
Impact of Long-Term Fertilization on Community Structure of Ammonia Oxidizing and Denitrifying Bacteria Based on amoA and nirK Genes in a Rice Paddy from Tai Lake Region, China. Journal of Integrative Agriculture, 13(10): 2286-2298.
|
| Alden L, Demoling F, Baath E. 2001. Rapid method ofdetermining factors limiting bacterial growth in soil.Applied and Environmental Microbiology, 67, 1830-1838Aulakh M S, Khera T S, Doran J W, Bronson K F. 2001.Denitrification, N2O and CO2 fluxes in rice-wheat croppingsystem as affected by crop residues, fertilizer N and legumegreen manure. Biology and Fertility of Soils, 34, 375-389Avrahami S, Conrad R. 2003. Patterns of community changeamong ammonia oxidizers in meadow soils upon longtermincubation at different temperatures. Applied andEnvironmental Microbiology, 10, 6152-6164Avrahami S, Conrad R, Braker G. 2002. Effect of soilammonium concentration on N2O release and on thecommunity structure of ammonia oxidizers and denitrifiers.Applied and Environmental Microbiology, 68, 5685-5692Barnard R, Leadley P W. 2005. Global change, nitrification,and denitrification: A review. Global BiogeochemicalCycles, 19, GB1007, doi: 10.1029/2004GB002282Bárta J, Melichová T, Van?k Daniel, Picek T. Šantr??kováH. 2010. Effect of pH and dissolved organic matter on theabundance of nirK and nirS denitrifiers in spruce forestsoil. Biogeochemistry, 101, 123-132Belser L W. 1979. Population ecology of nitrifying bacteria.Annual Review of Microbiology, 33, 309-333Cai Y F, Peng C, Zhao S Q, Cai A H, Li Y T. 2012. Balancedfertilization improved soil ammonia-oxidizing bacterialcommunity in latosolic red soil. Acta AgriculturaeScandinavica (Section B, Soil & Plant Science), 62, 531-540Chen Z, Luo X Q, Hu R G, Wu M N, Wu J S, Wei W X. 2010.Impact of long-term fertilization on the composition ofdenitrifier communities based on nitrite reductase analysesin a paddy soil. Microbial Ecology, 60, 850-861Chen Z, Yuan H Z, Wu J S, Wei W X. 2009. Activity andcomposition of the denitrifying bacterial communityrespond differently to long-term fertilization. ActaEcologica Sinica, 29, 5923-5929 (in Chinese)Chu H Y, Fujii T, Morimoto S, Lin X G, Yagi K, Hu J L, ZhangJ B. 2007. Community structure of ammonia-oxidizingbacteria under long-term application of mineral fertilizerand organic manure in a sandy loam soil. Applied andEnvironmental Microbiology, 73, 485-491Cruz A F, Hame C, Hanson K, Selles F, Zentner R P. 2009.Thirty-seven years of soil nitrogen and phosphorus fertilitymanagement shapes the structure and function of the soil microbial community in a Brown Chernozem. Plant andSoil, 315, 173-184David T, David W, Johanner K. 1996. Productivity andsustainability influenced by biodiversity in grasslandecosystems. Nature, 379, 718-720Dick R P. 1992. A review: long-term effects of agriculturalsystems on soil biochemical and microbial parameters.Agriculture, Ecosystems and Environment, 40, 25-36Enwall K, Nyberg K, Bertilsson S, Cederlund H, StenströmJohn, Hallin S. 2007. Long-term impact of fertilizationon activity and composition of bacterial communitiesand metabolic guilds in agricultural soil. Soil Biology &Biochemistry, 39, 106-115Enwall K, Philippot L, Hallin S. 2005. Activity andcomposition of the denitrifying bacterial communityrespond differently to long-term fertilization. Applied andEnvironmental Microbiology, 71, 8335-8343Fan F L, Yang Q B, Li Z J, Wei D, Cui X A, Liang Y C. 2011.Impacts of organic and inorganic fertilizers on nitrificationin a cold climate soil are linked to the bacterial ammoniaoxidizer community. Microbial Ecology, 62, 982-990Gong Z T. 1999. Chinese Soil Taxonomy, Theory Approachesand Application. Science Press, Beijing. pp. 160-165 (inChinese)He J Z, Hu H W, Zhang L M. 2012. Current insights into theautotrophic thaumarchaeal ammonia oxidation in acidicsoils. Soil Biology & Biochemistry, 55, 146-154He J Z, Shen J P, Zhang L M, Zhu Y G, Zheng Y M, Xu MM, Di H J. 2007. Quantitative analyses of the abundanceand composition of ammonia-oxidizing bacteria andammonia-oxidizing archaea of a Chinese upland red soilunder long-term fertilization practices. EnvironmentalMicrobiology, 9, 2364-2374Henry S, Baudoin E, López-Gutiérrez J C, Martin-LaurentF, Brauman A, Philippot L. 2004. Quantification ofdenitrifying bacteria in soils by nirK gene targeted realtimePCR. Journal of Microbiological Methods, 59,327-335Jin Z J, Pan G X, Liu X Y, Li L Q. 2013. Community structurecharacters and differences of N2-fixing and CO2-fixingbacteria under long-term fertilization in paddy soils ofTailake region, China. Acta Metallurgica Sinica, 19, 86-96 (in Chinese)Kandeler E, Deiglmayr K, Tscherko D, Bru D, Philippot L.2006. Abundance of narG, nirS, nirK, and nosZ genesof denitrifying bacteria during primary successions of aglacier foreland. Applied and Environmental Microbiology,72, 5957-5962 Kleineidam K, Sharma S, Kotzerke A, Heuer H, Thiele-BruhnS, Smalla K, Wilke B-M, Schloter M. 2010. Effect ofsulfadiazine on abundance and diversity of denitrifyingbacteria by determining nirK and nirS genes in two arablesoils. FEMS Microbiology Ecology, 60, 703-707Kong A Y Y, Hristova K, Scow K M, Six J. 2010. Impacts ofdifferent N management regimes on nitrifier and denitrifiercommunities and N cycling in soil microenvironments. SoilBiology & Biochemistry, 42, 1523-1533Li Y L, Zhang Y L, Hu J, Shen Q R. 2007. Contribution ofnitrification happened in rhizospheric soil growing withdifferent rice cultivars to N nutrition. Biology and Fertilityof Soils, 43, 417-425Liu D W, Liu X Y, Li L Q, Pan G X, David C, TippkötterR. 2011. SOC accumulation in paddy soils under longtermagro-ecosystem experiments from South China. VI.Changes in microbial community structure and respiratoryactivity. Biogeosciences Discuss, 8, 1529-1554Maeda K, Morioka R, Hanajima D, Osada T. 2010. The impactof using mature compost on nitrous oxide emission andthe denitrifier community in the cattle manure compostingprocess. FEMS Microbiology Ecology, 59, 25-36Miller M N, Zebarth B J, Dandie C E, Burton D L, Goyera C,Trevors J T. 2008. Crop residue influence on denitrification,N2O emissions and denitrifier community abundance insoil. Soil Biology & Biochemistry, 40, 2553-2562Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schafer H,Wawer C. 1997. Denaturing gradient gel electrophoresis(DGGE) in microbial ecology. In: Akkermans A D L,van Elsas J D, de Bruijn F J, eds., Molecular MicrobialEcology Manual. Kluwer Academic Publishers, Dordrecht,The Netherlands. p. 1-27Okano Y, Hristova K R, Leutenegger C M, Jackson L E,Denison R F, Gebreyesus B, Lebauer D, Scow K M.2004. Application of real-time PCR to study effects ofammonium on population size of ammonia-oxidizingbacteria in soil. Applied and Environmental Microbiology,70, 1008-1016Pan G X, Li L Q, Wu L S, Zhang X H. 2003. Storage andsequestration potential of topsoil organic carbon in China‘spaddy soils. Global Change Biology, 10, 79-92Pan G X, Smith P, Pan W N. 2009a. The role of soil organicmatter in maintaining the productivity and yield stability ofcereals in china. Agriculture Ecosystems and Environment,129, 344-348Pan G X, Zhou P, Li Z P, Smith P, Li L Q, Qiu D S, Zhang X H,Xu X B, Shen S Y, Chen X M. 2009b. Combined inorganic/organic fertilization enhances N efficiency and increasesrice productivity through organic carbon accumulation ina rice paddy from the Tai Lake region, China. Agriculture,Ecosystem and Environment, 131, 274-280Phillips C J, Harris D, Dollhopf S L, Gross K L, Prosser JI, Eldor A P. 2000. Effects of agronomic treatments onstructure and function of ammonia-oxidizing communities.Applied and Environmental Microbiology, 66, 5410-5418Rotthauwe J H, Witzel K P, Liesack W. 1997. The ammoniamonooxygenase structural gene amoA as a functionalmarker, molecular fine scale analysis of natural ammoniaoxidizingpopulations. Applied and EnvironmentalMicrobiology, 63, 4704-4712Schmidt I. 2009. Chemoorganoheterotrophic growth ofNitrosomonas europaea and Nitrosomonas eutropha.Current Microbiology, 59, 130-138Schmidt M W I, Torn M S, Abiven S, Dittmar T, Guggenberger G, Janssens I A, Kleber M, Kögel-Knabner I, LehmannJ, Manning D A C, Nannipieri P, Rasse D P, Weiner S,Trumbore S E. 2011. Persistence of soil organic matter asan ecosystem property. Nature, 478, 49-56Soil Survey Staff, USDA. 1994. Keys to Soil Taxonomy.6th ed. United States Department of Agriculture, SoilConservation Service, USA. pp. 161-186Sooksa-Nguan T, Thies J E, Gypmantasiri P, Boonkerd N,Teaumroong N. 2009. Effect of rice cultivation systemson nitrogen cycling and nitrifying bacterial communitystructure. Applied Soil Ecology, 43, 139-149Szukics U, Hackl E, Zechmeister-Boltenstern S, Sessitsch A.2009. Contrasting response of two forest soils to nitrogeninput, rapidly altered NO and N2O emissions and nirKabundance. Biology and Fertilizer of Soils, 45, 855-863Throbäck I N, Enwall K, Jarwis A, Hallin S. 2004. ReassessingPCR primers targeting nirS, nirK and nosZ genes forcommunity surveys of denitrifying bacteria with DGGE.FEMS Microbiology Ecology, 49, 401-417Vanderheijden M G A, John N K, Ursic M, Moutoglis P,Streitwolf-Engel R, Boller T, Wiemken A, Sanders IR. 1998. Mycorrhizal fungal diversity determines plantbiodiversity, ecosystem variability and productivity.Nature, 396, 69-72Wallenstein M D, Myrold D D, Firestone M, Voytek M. 2006.Environmental controls on denitrifying communities anddenirtrification rate, insight from molecular methods.Ecological Applications, 16, 2143-2152Wang C J, Pan G X, Tian Y G, Li L Q, Zhang X H, Han XJ. 2010. Changes in cropland topsoil organic carbon withdifferent fertilizations under long-term agro-ecosystemexperiments across mainland China. Science China (LifeSciences), 53, 858-867Wang S X, Liang X Q, Luo Q X，Fan F, Chen Y X, Li Z Z,Sun H X, Dai T F, Wan J N, Li X J. 2012. Fertilizationincreases paddy soil organic carbon density. Journalof Zhejiang University-SCIENCE B (Biomedicine &Biotechnology), 13, 274-282Wang Y N, Ke X B, Wu L Q, Lu Y H. 2009. Communitycomposition of ammonia-oxidizing bacteria and archaeain rice field soil as affected by nitrogen fertilization.Systematic and Applied Microbiology, 32, 27-36Wessén E, Nybergb K, Janssonc J K, Hallina S. 2010.Responses of bacterial and archaeal ammonia oxidizersto soil organic and fertilizer amendments under long-termmanagement. Applied Soil Ecology, 45, 193-200Wu J S. 2011. Carbon accumulation in paddy ecosystemsin subtropical China, evidence from landscape studies.European Journal of Soil Science, 62, 29-34Xu X B, Xu X D, Chu Q H, Qiu D S. 1999. Influence ofdifferent fertilizations in crop yield and soil fertility. In:Soil Science Society of Jiangsu, ed., Soil Science andTechnology of Jiangsu Facing the 21th Century. HohaiUniversity Press, Nanjing. pp. 107-110 (in Chinese)Yu Z N, Li F D, He S J. 1996. Experiment And Techniqueof Agricultural Microbiology. China Agriculture Press,Beijing. pp. 125-126 (in Chinese)Zhang P J, Li L Q, Pan G X, Zhang J W. 2004. Influence oflong- term fertilizer management on topsoil microbialbiomass and genetic diversity of a paddy soil from theTai Lake region, China. Acta Ecologica Sinica, 24, 2818-2824 (in Chinese)Zhang P J, Zheng J F, Pan G X, Zhang X H, Li L Q, TippkötterR. 2007. Changes in microbial community structure andfunction with in particle size fractions of a paddy soilunder different long-term fertilization treatments fromthe Tai Lake region, China. Colloids and Surfaces B:Biointerfaces, 58, 264-270Zhang W J, Xu M G, Wang X J, Huang Q H, Nie J, Li Z Z,Li S L, Hwang S W, Lee K B. 2012. Effects of organicamendments on soil carbon sequestration in paddy fieldsof subtropical China. Journal of Soils and Sediments, 12,457-470Zheng J F, Zhang P J, Pan G X, Li L Q, Zhang X H. 2008.Effect of long-term different fertilization on methaneoxidation potential and diversity of methanotrophs ofpaddy soil. Acta Ecologica Sinica, 28, 4864-4872 (inChinese)Zhong W H, Cai Z C, Yin L C, Zhang H. 2007. The effectsof the long-term application of inorganic fertilizers onmicrobial community diversity in rice-planting red soilas studied by PCR-DGGE. Acta Ecologica Sinica, 27,4011-4018 (in Chinese) |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
