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http://dx.doi.org/10.7857/JSGE.2016.21.4.050

Microbial Activity of Ammonia Oxidizing Bacteria and Ammonia Oxidizing Archaea in the Rice Paddy Soil in Wang-gung Area of Iksan, Korea  

Kim, Hyun-su (Department of Earth and Environmental Sciences, Chonbuk National University)
Publication Information
Journal of Soil and Groundwater Environment / v.21, no.4, 2016 , pp. 50-59 More about this Journal
Abstract
Spatial and temporal changes in nitrification activities and distribution of microbial population of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in paddy soils were investigated. Soil samples were collected in March and October 2015 from rice paddy with and without the presence of confined animal feeding operations. Incubation experiments and quantitative polymerase chain reaction showed that AOA's contribution to nitrification kinetics was much higher in locations where organic nitrogen in animal waste is expected to significantly contribute to overall nitrogen budget, and temporal variations in nitrification kinetics were much smaller for AOA than AOB. These differences were interpreted to indicate that different microbial responses of two microbial populations to the types and concentrations of nitrogen substrates were the main determining factors of nitrification processes in the paddy soils. The copy numbers of ammonium monooxygenase gene showed that AOA colonized the paddy soils in higher numbers than AOB with stable distribution while AOB showed variation especially in March. Although small in numbers, AOB population turned out to exert more influence on nitrification potential than AOA, which was attributed to higher fluctuation in AOB cell numbers and nitrification reaction rate per cells.
Keywords
Nitrification; Rice paddy; Ammonia oxidizing bacteria; Ammonia oxidizing archaea; Ammonia monooxygenase;
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1 Ai, C., Liang, G., Sun, J., Wang, X., He, P., and Zhou, W., 2013, Different roles of rhizo-sphere effect and long-term fertilization in the activity and community structure of ammonia oxidizers in a calcareous fluvo-aquic soil, Soil Biol. Biochem., 57, 30-42.   DOI
2 Alves, R.J.E., Wanek, W., Zappe, A., Richter, A., Svennin, M.M., Schleper, C., and Urich, T., 2013, Nitrification rates in arctic soils are associated with functionally distinct populations of ammonia-oxdizing archaea, ISME J., 7, 1620-1631.   DOI
3 Booth, M.S., Stark, J.M., and Rastetter, E., 2005, Controls on nitrogen cycling in terrestrial ecosystem: a synthetic analysis of literature data, Ecol. Monogr., 75, 139-157.   DOI
4 Buresh, R.J. and De, Datta, S.K., 1990, Denitrification losses from puddle rice soils in the tropics, Biol. Fert. Soils, 9, 1-13.   DOI
5 Gubry-Rangin, C., Nicol, G.W., and Prosser, J.I., 2010, Archaea rather than bacteria control nitrification in two agricultural acidic soils, FEMS Microbiol. Ecol., 74, 566-574.   DOI
6 Habteselassie, M.Y., Xu, L., and Norton, J.M., 2013, Ammoniaoxidizer communities in an agricultural soil treated with contrasting nitrogen sources, Front. Microbiol., 4, 326.
7 Harrison, M.D., Groffman, P.M., Mayer, P.M., Kaushal, S.S., and Newcomer, T.A., 2011, Denitrification in alluvial wetlands in an urban landscape, J. Environ. Qual., 40, 634-646.   DOI
8 Hatzenpichler, R., Lebedeva, E.V., Spieck, E., Stoecker, K., Richter, A., Daims, H., and Wagner, M., 2008, A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring, Proc. Natl. Acad. Sci. U.S.A., 105, 2134-2139.   DOI
9 Jiang, Q.Q. and Bakken, L.R., 1999, Comparison of Nitrosospira strains isolated from terrestrial environments, FEMS Microbiol. Ecol., 30, 171-186.   DOI
10 Jiang, H., Huang, L., Deng, Y., Wang, S., Zhou, Y., Liu, L., and Dong, H., 2014a, Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China, Applied and Environ. Microbiol., 80, 5593-5602.   DOI
11 Jiang, Y., Jin, C., and Sun, B., 2014b, Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil, Environ. Microbiol., 16, 3083-3094   DOI
12 Kim, H. and Jaffé, P., 2007, Spatial distribution and physiological state of bacteria in a sand column experiment during the biodegradation of toluene, Water Res., 41, 2089-2100.   DOI
13 Konneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A., 2005, Isolation of an autotropic ammonia-oxidizing marine archaeon, Nature, 437, 543-546.   DOI
14 Lan, T., Han, Y., Roelcke, M., Nieder, R., and Cai, Z., 2013, Effects of the nitrification inhibitor dicyandiamide (DCD) on gross N transformation rates and mitigating N2O emission in paddy soils, Soil Biol. Biochem., 67, 174-182.   DOI
15 Lehtovirta-Morley, L.E., Stoecker, K., Vilcinskas, A., Prosser, J.J., and Nichol, G.W., 2011, Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil, Proc. Natl. Acad. Sci. U.S.A., 108(38), 15892-15897.   DOI
16 Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., Prosser, J.I., Schuster, S.C., and Schleper, C., 2006, Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature, 442, 806-809.   DOI
17 Martens-Habbena, W., Berube, P.M., Urakawa, H., de la Torre, J.R., and Stahl, D.A., 2009, Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria, Nature, 461, 976-979.   DOI
18 Nicolaisen, M.H., Risgaard-petersen, N., Revsbech, N.P., Reichardt, W., and Ramsing, N.B., 2004, Nitrification-denitrification dynamics and community structure of ammonia oxidizing bacteria in a high yield irrigated Philippine rice field, FEMS Microbiol. Ecol., 49, 359-369.   DOI
19 Myrold, D.D., Zeglin, L.H., and Jansson, J.K., 2014, The potential of metagenomics approaches for understanding soil microbial processes, Soil Sci. Soc. Am. J., 78, 3-10.   DOI
20 Nicol, G.W., Leininger, S., Schleper, C., and Prosser, J.I., 2008, The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria, Environ. Microbiol., 10, 2966-2978.   DOI
21 Norton, J.M. and Stark, J.M., 2011, Regulation and measurement of nitrification in terrestrial systems, Methods in Enzymol., 486, 343-368.   DOI
22 Offre, P., Prosser, J.I., and Nicol, G.W., 2009, Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene, FEMS Microbiol. Ecol., 70, 99-108.   DOI
23 Okano, Y., Hristova, K.R., Leutenegger, C.M., Jackson, L.E., Denison, R.F., and Gebreyesus, B., 2004, Application of realtime PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil, Appl. Environ. Microbiol., 70, 1008-1016.   DOI
24 Phongpan, S. and Mosier, A.R., 2003, Effect of crop residue management on nitrogen dynamics and balance in a lowland rice cropping system, Nutr. Cycl. Agroecosys., 66, 133-142.   DOI
25 Rust, C.M., Aelion, C.M., and Flora, J.R.V., 2000, Control of pH during denitrification in sub-surface sediment microcosms using encapsulated phosphate buffer, Water Res., 34(5), 1447-1454.   DOI
26 Taylor, A.E., Zeglin, L.H., Wanzek, T.A., Myrold, D.D., and Bottomley, P.J., 2012, Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials, ISME J., 6, 2024-2032.   DOI
27 Schleper, C. and Nicol, G.W., 2010, Ammonia-oxidising archaea - physiology, ecology and evolution, In: R.K. Poole (ed.), Advances in Microbal Physiology, vol. 57, Academic Press Ltd-Elsevier Science Ltd, London, p. 1-41.
28 Shen, J.P., Zhang, L.M., Zhu, Y.G., Zhang, J.B., and He, J.Z., 2008, Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam, Environ. Microbiol., 10, 1601-1611.   DOI
29 Taylor, A.E., Vajrala, N., Giguere, A.T., Gitelman, A.I., Arp, D.J., Myrold, D.D., Saya-vedra-Soto, L., and Bottomley, P.J., 2013, Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria, Appl. Environ. Microbiol., 79, 6544-6551.   DOI
30 Tourna, M., Stieglmeier, M., Spang, A., Könneke, M., Schintlmeister, A., Urich, T., Engel, M., Schloter, M., Wagner, M., Richter, A., and Schleper, C., 2011, Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil, Proc. Natl. Acad. Sci. U.S.A., 108, 8420-8425.   DOI
31 Treusch, A., Leininger, S., Kletzin, A., Schuster, Sc.R., Klenk, H.P., and Schleper, C., 2005, Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling, Environ. Microbiol., 7, 1985-1995.   DOI
32 Wessen E., Soderstrom, M, Stenberg, M., Bru, D., Hellman, M., Welsh, A., Thomsen, F., Klemedtson, L., Philippot, L., and Hallin, S., 2011, Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning, ISME J., 5, 1213-1225.   DOI
33 Zhang, L.-M., Offre, P.R., He, J.-Z., Verhamme, D.T., Nicol, G.W., and Prosser, J.I., 2010, Autotrophic ammonia oxidation by soil thaumarchaea, Proc. Natl. Acad. Sci. U.S.A., 107, 17240-17245.   DOI
34 Wang, Y., Ke, X., Wu, L., and Lu, Y., 2009, Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization, Syst. Appl. Microbiol., 32, 27-36.   DOI