|Table of Contents|

Research advances on microbial function in soil ammonifying process(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

2014 02
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Research advances on microbial function in soil ammonifying process
1 College of Natural Resource and Environment, Key Laboratory of Plant Nutrition and Agri-environment of Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China 2 State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Northwest A&F University, Yangling 712100, China
ammonifying process ammonifier carbon to nitrogen ratio rate-limiting step high-throughput sequencing

Inorganic nitrogen which comes from soil nitrogen mineralization is the main nitrogen source for plant. Ammonifying process is the first step of nitrogen mineralization, in which microbes play an important role. This paper discussed the effects of microbes in ammonifying process from three aspects: the microbial action mechanism of degrading soil organic nitrogen into ammonia, the influencing factors including available carbon to nitrogen ratio, protease and microbial community structure, and some latest techniques for microbial research. Some researches found that the depolymerization of high molecular weight soluble organic nitrogen is likely the rate-limiting step in ammonifying process; soil microbial biomass nitrogen may be the direct and main source of microbial available organic nitrogen; at the same time, soil available carbon to nitrogen ratio has a significant effect on the production of ammonium. In the end, we introduced some new molecular biology techniques, especially high-throughput sequencing for research of soil microbes, and suggested the unsolved problems and possible future research direction.


1 周志华, 肖化云, 刘丛强. 土壤氮素生物地球化学循环的研究现状与进展[J]. 地球与环境, 2004, 32 (3-4): 21-26 [Zhou ZH, Xiao HY, Liu CQ. Research status and advances in biogeochemical cycling nitrogen in soils [J]. Earth Environ, 2004, 32 (3-4): 21-26]
2 Jones DL, Shannon D, Murphy DV, Farrar J. Role of dissolved organic nitrogen (DON) in soil N cycling in grassland soils [J]. Soil Biol Biochem, 2004, 36 (5): 749-756
3 Schimel JP, Bennett J. Nitrogen mineralization: challenges of a changing paradigm [J]. Ecol Soc Am, 2004, 85 (3): 591-602
4 David L, Jones KK. Soil amino acid turnover dominates the nitrogen flux in permafrost-dominated taiga forest soils [J]. Soil Biol Biochem, 2002, 34: 209-219
5 Jones DL, Kielland K. Amino acid, peptide and protein mineralization dynamics in a taiga forest soil [J]. Soil Biol Biochem, 2012, 55: 60-69
6 Roberts P, Stockdale R, Khalid M, Iqbal Z, Jones DL. Carbon-to-nitrogen ratio is a poor predictor of low molecular weight organic nitrogen mineralization in soil [J]. Soil Biol Biochem, 2009, 41 (8): 1750-1752
7 Mengel K. Turnover of organic nitrogen in soils and its availability to crops [J]. Plant Soil, 1996, 181: 83-93
8 钱佩源, 吴豪森. 水稻土氮素矿化的微生物学活性研究[J]. 上海农学院学报, 1985, 3 (1): 7-13 [Qian PY, Wu HS. Studies on microbiological activities of nitrogen mineralization in paddy soils [J]. J Shanghai Agric Coll, 1985, 3 (1): 7-13]
9 Stark CH, Condron LM, O’Callaghan M, Stewart A, Di HJ. Differences in soil enzyme activities, microbial community structure and short-term nitrogen mineralisation resulting from farm management history and organic matter amendments [J]. Soil Biol Biochem, 2008, 40 (6): 1352-136
10 Tian L, Dell E, Shi W. Chemical composition of dissolved organic matter in agroecosystems: correlations with soil enzyme activity and carbon and nitrogen mineralization [J]. Appl Soil Ecol, 2010, 46 (3): 426-435
11 Thomas M, Schmidt MS. Topics in Ecological and Environmental Microbiology [M]. New York: Academic Press, 2011
12 Zaman M, Di HJ, Cameron KC, Frampton CM. Gross nitrogen mineralization and nitrification rates and their relationships to enzyme activities and the soil microbial biomass in soils treated with dairy shed effluent and ammonium fertilizer at different water potentials [J]. Biol Fertil Soils, 1999, 29: 178-186
13 Singh DK, Kumar S. Nitrate reductase, arginine deaminase, urease and dehydrogenase activities in natural soil (ridges with forest) and in cotton soil after acetamiprid treatments [J]. Chemosphere, 2008, 71 (3): 412-418
14 Badalucco L, Kuikman PJ, Nannipieri P. Protease and deaminase activities in wheat rhizosphere and their relation to bacterial and protozoan populations [J]. Biol Fertil Soils, 1996, 23: 99-104
15 Shah S, Li JP, Moffatt BA, Glick BR. Isolation and characterization of ACC deaminase genes from two different plant growth-promoting rhizobacteria [J]. Microbiol J Can, 1998, 44: 833-843
16 普雪斯科特. 微生物学[M]. 沈萍, 彭珍荣主译. 5版. 北京: 高等教育出版社, 2003
17 Nuutinen JT, Timonen S. Identification of nitrogen mineralization enzymes, L-amino acid oxidases, from the ectomycorrhizal fungi Hebeloma spp. and Laccaria bicolor [J]. Brit Mycol Res, 2008, 112: 1453-1464
18 马迪根, 马丁克, 帕克. 微生物生物学[M]. 杨文博等译. 8版. 北京: 科学出版社, 2001
19 Satti P, Mazzarino MJ, Gobbi M, Funes F, Roselli L, Fernandez H. Soil N dynamics in relation to leaf litter quality and soil fertility in north-western Patagonian forests [J]. J Ecol, 2003, 91: 173-181
20 沈其荣, 史瑞和. 土壤预处理对不同起源氮矿化的影响[J]. 南京农业大学学报, 1991, 14 (1): 54-58 [Shen QR, Shi RH. The effect of soil pretreatment on the mineralization of nitrogen deprived from different forms [J]. J Nanjing Agric Univ, 1991, 14 (1): 54-58]
21 Okano S, Nishio M, Sawada Y. Turnover rate of soil biomass nitrogen in the root mat layer of pasture [J]. Plant Nutr Soil Sci, 1987, 33 (3): 373-386
22 Marumoto T, Anderson JPE, Domsch KH. Decomposition of 14 C- and 15 N-labelled microbial cells in soil [J]. Soil Biol Biochem, 1982, 14: 461-467
23 Holems WE, Zak DR. Soil microbial biomass dynamics and net nitrogen mineralization in northern hardwood ecosystems [J]. Soil Sci Soc Am, 1994, 58: 238-243
24 张成霞,南志标. 土壤微生物生物量的研究进展[J]. 草业科学, 2010, 27 (6): 50-57 [Zhang CX, Nan ZB. Research progress of soil microbial biomass in China [J]. Pratacul Sci, 2010, 27 (6): 50-57]
25 Zak DR, Holmes WE, White DC, Peacock AD, Tilman D. Plant diversity, soil microbial communities, and ecosystem function: are there any links? [J] Ecology, 2003, 84 (4): 2042–2050
26 Henry HAL, Juarez JD, Field CB, Vitousek PM. Interactive effects of elevated CO2, N deposition and climate change on extracellular enzyme activity and soildens ity fractionation in a California annual grassland [J]. Global Change Biol, 2005, 11: 1808-1815
27 Allison SD, Treseder KK. Warming and drying suppress microbial activity and carbon cycling in boreal forest soils [J]. Global Change Biol, 2008, 14: 2898-2909
28 Alef K, Kleiner D. Applicability of arginine ammonification as indicator of microbial activity in different soils [J]. Biol Fertil Soils, 1987, 5: 148-151
29 Schmidt BHM, Kalbitz K, Braun S, Fu? R, McDowell WH, Matzner E. Microbial immobilization and mineralization of dissolved organic nitrogen from forest floors [J]. Soil Biol Biochem, 2011, 43 (8): 1742-1745
30 Geisseler D, Horwath WR. Regulation of extracellular protease activity in soil in response to different sources and concentrations of nitrogen and carbon [J]. Soil Biol Biochem, 2008, 40: 3040-3048
31 Kuzyakov Y, Friedel JK, Stahr K. Review of mechanisms and quantification of priming effects [J]. Soil Biol Biochem, 2000, 32: 1485-1498
32 Burns RG, DeForest JL, Marxsen J, Sinsabaugh RL, Stromberger ME, Wallenstein MD, Weintraub MN, Zoppini A. Soil enzymes in a changing environment: current knowledge and future directions [J]. Soil Biol Biochem, 2013, 58: 216-234
33 Asmar F, Eiland F, Nielsen NE. Effect of extracellular-enzyme activities on solubilization rate of soil organic nitrogen [J]. Biol Fertil Soils, 1994, 17: 32-38
34 Cusack DF. Soil nitrogen levels are linked to decomposition enzyme activities along an urban-remote tropical forest gradient [J]. Soil Biol Biochem, 2013, 57: 192-203
35 Bach HJ, Munch JC. Identification of bacterial sources of soil peptidases [J]. Biol Fertil Soils, 2000, 31: 219-224
36 Watanabe K, Hayano K. Source of soil protease based on the splitting sites of a polypeptide [J]. Soil Sci Plant Nutr, 1994, 40 (4): 697-701
37 Nygren CMR, Edqvist J, Elfstrand M, Heller G, Taylor FS. Detection of extracellular protease activity in different species and genera of ectomycorrhizal fungi [J]. Mycorrhiza, 2007, 17 (3): 241-248
38 周巧红, 吴振斌, 付贵萍, 成水平,贺锋. 人工湿地基质中酶活性和细菌生理群的时空动态特征[J]. 环境科学, 2005, 26 (6): 108-112 [Zhou QH, Wu ZB, Fu GP, Cheng SP, He F. Temporal and spatial characteristics of substrate enzyme activities and bacteria physiological groups in constructed wetland [J]. Environ Sci, 2005, 26 (6): 108-112]
39 Sepers ABJ. Diversity of ammonifying bacteria [J]. Hydrobiologia, 1981, 83: 343-350
40 赵满兴, Kalbitz K, 周建斌. 黄土区几种土壤培养过程中可溶性有机氮的变化及其与土壤矿化氮的关系[J]. 水土保持学报, 2008, 22 (4): 122-127 [Zhao MX, Kalbitz K, Zhou JB. Dynamics of soluble organic nitrogen and its relation to mineralization of soil organic nitrogen during incubation of several soils in Loess Region [J]. J Soil Water Conserv, 2008, 22 (4): 122-127]
41 Boyle SA, Yarwood RR, Bottomley PJ, Myrold DD. Bacterial and fungal contributions to soil nitrogen cycling under Douglas fir and red alder at two sites in Oregon [J]. Soil Biol Biochem, 2008, 40 (2): 443-451
42 王娟, 戴习林, 宋增福, 潘迎捷, 张庆华. 一株氨化细菌的分离, 鉴定及氨氮降解能力的初步分析[J]. 水生生物学报, 2010, 34 (6): 1199-1201[Wang J, Dai XL, Song ZF, Pan YJ, Zhang QH. Isolation and identification of ammonifying bacteriun and characteristics of degrading NH3-N [J]. Acta Hydrobiol Sin, 2010, 34 (6): 1199-1201]
43 张文艺, 李秋艳, 赵婷婷, 李定龙, 姚立荣, BAF反应器中氨化细菌的筛选与氨化特性分析[J]. 环境工程学报, 2011, 5 (12): 2890-2894 [Zhang WY, Li QY, Zhao TT, Li DL, Yao LR. Isolation of amonifying bacteria from BAF reactor and analysis on amination characterization [J]. Tech Equip Environ Pollut Control, 2011, 5 (12): 2890-2894]
44 马桂珍, 暴增海, 王淑芳, 吴少杰, 付泓润, 葛平华, 高产蛋白酶细菌的分离筛选及其种类鉴定[J]. 食品科学, 2011, 32 (21): 183-187 [Ma GZ, Bao ZH, Wang SF, Wu SJ, Fu HR, Ge PH. Screening and identification of high protease-producing bacteria [J]. Food Sci, 2011, 32 (21): 183-187]
45 Josephine FS, Ramya VS, Devi N, Ganapa SB, Siddalingeshwara KG, Venugopal N, Vishwanatha T. Isolation, production and characterization of protease from Bacillus sp. isolated from soil sample [J]. J Microbiol Biotechnol Res, 2012, 2 (1): 163-168
46 Garnier P, Neel C, Aita C, Recous S, Lafolie F, Mary B. Modelling carbon and nitrogen dynamics in a bare soil with and without straw incorporation [J]. Eur J Soil Sci, 2003, 54: 555-568
47 Smith JL, Norton JM, Paul EA. Decomposition of 14C- and 15N-labeled organisms in soil under anaerobic conditions [J]. Plant Soil, 1989, 116: 115-118
48 Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G. Microbial diversity and soil functions [J]. Eur J Soil Sci, 2003, 54: 655-670
49 Fuka MM, Engel M, Hagn A, Munch JC, Sommer M, Schloter M. Changes of diversity pattern of proteolytic bacteria over time and space in an agricultural soil [J]. Microb Ecol, 2009, 57 (3): 391-401
50 Petersen DG, Blazewicz SJ, Firestone M, Herman DJ, Turetsky M, Waldrop M. Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska [J]. Environ Microbiol, 2012, 14 (4): 993-1008
51 王兴春, 杨致荣, 王敏, 李玮、李生才. 高通量测序技术及其应用[J]. 中国生物工程杂志, 2012, 32 (1): 109-114 [Wang XC, Yang ZR, Wang M, Li W, Li SC. High-throughput sequencing technology and its application [J]. China Biotechnol, 2012, 32 (1): 109-114]
52 Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW. Pyrosequencing enumerates and contrasts soil microbial diversity [J]. ISME J, 2007, 1 (4): 283-290
53 Chu HY, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes [J]. Environ Microbiol, 2010, 12 (11): 2998-3006
54 Bach HJ, Hartmann A, Schloter M, Munch JC. PCR primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil [J]. J Microbiol Methods, 2000, 44: 173-182
55 Rao MB, Tanksale AM, Ghatge MS, Deshpande VV. Molecular and biotechnological aspects of microbial proteases [J]. Microbiol Mol Biol Rev, 1998, 62 (3): 597-635
56 Sakurai M, Suzuki K, Onodera M, Shinano T, Osaki M. Analysis of bacterial communities in soil by PCR–DGGE targeting protease genes [J]. Soil Biol Biochem, 2007, 39 (11): 2777-2784
57 Yu K, Zhang T. Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge [J]. PLoS ONE, 2012, 7 (5): 1-13
58 Zakrzewski M, Goesmann A, Jaenicke S, Junemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sorensen S, Puhler A, Schluter A. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing [J]. J Biotechnol, 2012, 158 (4): 248-258
59 Wang XC, Niu QW, Teng C, Li C, Mu JY, Chua NH, Zuo JR. Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis [J]. Cell Res, 2009, 19 (2): 224-235
60 吕昌勇, 陈朝银, 葛锋, 刘迪秋, 孔祥君. 微生物分子生态学研究方法的新进展[J]. 中国生物工程杂志, 2012, 32 (8): 111-118 [Lü CY, Chen CY, Ge F, Liu DQ, Kong XJ. The new development of the research method for molecular microbial ecology [J]. China Biotechnol, 2012, 32 (8): 111-118]
61 Zhou JZ, Xue K, Xie JP, Deng Y, Wu L, Cheng XL, Fei SF, Deng SP, He ZL, Van Nostrand JD. Microbial mediation of carbon-cycle feedbacks to climate warming [J]. Nat Climate Change, 2011, 2 (2): 106-110
62 He ZL, Xu MY, Deng Y, Kang S, Kellogg L, Wu LY, Nostrand JDV, Hobbie SE, Reich PB, Zhou JZ. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2 [J]. Ecol Lett, 2010, 13 (5): 564-575
63 Nannipieri P, Giagnoni L, Renella G, Puglisi E, Ceccanti B, Masciandaro G, Fornasier F, Moscatelli MC, Marinari S. Soil enzymology classical and molecular approaches [J]. Biol Fertil Soils, 2012, 48: 743-762


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