Effect of Long Term Fertilization on Microbial Biomass, Enzyme Activities, and Community Structure in Rice Paddy Soil

  • Lee, Chang Hoon (Division of Soil and Fertilizer, NAAS, RDA) ;
  • Kang, Seong Soo (Division of Soil and Fertilizer, NAAS, RDA) ;
  • Jung, Ki Youl (FunctionalCereal Crop Research Division, NCSI, RDA) ;
  • Kim, Pil Joo (Division of Applied Life Science (BK 21 Program), Gyeongsang National University)
  • Received : 2013.10.31
  • Accepted : 2013.11.18
  • Published : 2013.12.31


The effects of long-term fertilization on soil biological properties and microbial community structure in the plough layer in a rice paddy soil in southern Korea were investigated in relation to the continuous application of chemical fertilizers (NPK), straw based compost (Compost), combination these two (NPK + Compost) for last 40 years. No fertilization plot (Control) was installed for comparison. Though fertilization significantly improved rice productivity over control, the long-term fertilization of NPK and compost combination was more effective on increasing rice productivity and soil nutrient status than single application of compost or chemical fertilizer. All fertilization treatments had shown significant improvement in soil microbial properties, however, continuous compost fertilization markedly increased soil enzyme and microbial activities as compared to sole chemical fertilization. Results of microbial community structure, evaluated by EL-FAME (ester-linked fatty acid methyl esters) method, revealed big difference among Control, NPK, and Compost. However, both Compost and Compost+NPK treatments belonged to the same cluster after statistical analysis. The combined application of chemical fertilizer and organic amendments could be more rational strategy to improve soil nutrient status and promote soil microbial communities than the single chemical fertilizer or compost application.


Long-term fertilization;Paddy soil;Microbial community structure;FAMES


Supported by : National Academy Agricultural Science


  1. Yadav, R.L., B.S. Dwivedi, K. Prasad, O.K. Tomar, N.J. Shurpali, and P.S. Pandey. 2000. Yield trends, and changes in soil organic-C and available NPK in a long-term rice-wheat system under integrated use of manures and fertilizers. Field Crops Res. 68:219-246.
  2. Zelles, L., Q.Y. Bai, T. Beck, and F. Beese. 1992. Signature fatty acids in phospholipids and lipopolysacharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol. Biochem. 24:317-323.
  3. Zelles, L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterization of microbial communities in soil: a review. Biol. Fertil. Soils. 29:111-129.
  4. Allison, L.E. 1965. Organic carbon. In Methods of soil analysis, ed. C. A. Black, Madison, Wisc., ASA, pp. 1367-1376.
  5. Bossio, D.A., K.M. Scow, N. Gunapala, and K.J. Graham. 1998. Determinants of soil microbial communities: effects of agricultural management, season and soil type on phospholipid fatty acid profiles. Microbial Ecol. 36:1-12.
  6. Brookes, P.C., D.S. Powlson, and D.S. Jenkinson.1982. Measurement of microbial biomass phosphorus in soil. Soil Biol. Biochem. 14:319-329.
  7. Dawe, D., A. Dobermann, P. Moya, S. Abdulrachman, B. Singh, P. Lal, S.Y. Li, B. Lin, G. Panaullah, O. Sariam, Y. Singh, A. Swarup, P.S. Tan, and Q. X. Zhen. 2000. How widespread are yield declines in long-term rice experiments in Asia? Field Crops Res. 66:175-193.
  8. Dinesh, R., M.A. Suryanarayana, S. Ghosha, and T.E. Sheeja. 2004. Long-term influence of leguminous cover crops on the biochemical properties of a sandy clay loam Fluventic Sulfaquent in a humid tropical region of India. Soil Tillage Res. 77:69-77.
  9. Doran, J.W., and T.B. Parkin.1994. Defining and assessing soil quality. In Defining Soil Quality for a Sustainable Environment Doran, J.W., Coleman, D.C., Bezdicek, D.F., Stewart, B.A. (Eds.), Soil Science Society of America: Madison, Wisconsin, pp. 3-21.
  10. Duxbury, J.M., I.P. Abrol, R.K. Gupta, and K. Bronson. 2000. Analysis of long-term soil fertility experiment with rice-wheat rotation South Asia. In: Abrol, I.P., Bronson, K., Duxbury, J.M., Gupta, R.K. (Eds.), Long-term Soil Fertility Experiments in Rice-Wheat Cropping Systems. Rice Wheat Consortium Research Series 6. Rice-Wheat Consortium for the Indo-Gangetic Plains, New Delhi, India, pp. 7-12.
  11. Eivazi, E., and M.A. Tabatabai.1988. Glucosidases and galactosidases in soils. Soil Biol. Biochem. 20:601-606.
  12. Frostegard, A., and E. Baath. 1996. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol. Fertil. Soils. 22:59-65.
  13. Frostegard, A., E. Baath, and A. Tunlid.1993. Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol. Biochem. 25:723-730.
  14. Haynes, R.J., R. Tregurtha. 1999. Effects of increasing periods under intensive arable vegetable production on biological, chemical and physical indices of soil quality. Biol. Fertil. Soils. 28:259-266.
  15. Gregorich, E.G., M.R. Carter, D.A. Angers, C.M. Monreal, and B.H. Ellert. 1994. Towards a minimum data set to assess soil organic matter quality in agricultural soils. Can. J. Soil Sci. 74:367-385.
  16. Ibekwe, A.M., and A.C. Kennedy. 1998. Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils. Plant and Soil. 206:151-161.
  17. Islam, K.R., and P.R. Weil. 2000. Soil quality indictor properties in Mid-Atlantic Soils as influenced by conservation management. J. Soil Water Conserv. 55:69-78.
  18. Jenkinson, D.S. 1988. The determination of microbial biomass carbon and nitrogen in soil. In: Wilson, J.R. (Ed.), Advances in nitrogen cycling in agricultural ecosystems, C.A.B. International, Wallingford, U.K., pp. 368-386.
  19. Kennedy, A.C., and R.I. Papendick. 1995. Microbial characteristics of soil quality. J. Soil Water Conserv. 50: 243-248.
  20. Larson, W.F., and F.J. Pierce. 1991. Conservation and enhancement of soil quality. In Evaluation for Sustainable Land Management in the Developing World; Proceedings of the 12 International Board for Soil Resource and Management: Bangkok, Thailand; Vol. 2.
  21. Lee, S.B., C.H. Lee, K.Y. Jung, K.D. Park, D.K. Lee, and P.J. Kim. 2009. Changes of soil organic carbon and its fractions in relation to soil physical properties in a long-term fertilized paddy. Soil Tillage Res. 104:227-232.
  22. Madejon, E., P. Burgos, R. Lopez, and F. Cabrera. 2001. Soil enzymatic response to addition of heavy metals with organic residues, Biol. Fertil. Soils. 34:144-150.
  23. Marschner, P., E. Kandeler, and B. Marschner. 2003. Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol. Biochem. 35:453-461.
  24. Masciandaro, G., B. Ceccanti, and C. Garcia. 1997. Change in soil biochemical and cracking properties induced by "living mulch systems". Can. J. Soil Sci. 77:579-587.
  25. Nannipieri, P., B. Ceccanti, S. Cervelli, and P. Sequi. 1974. Use of pyrophosphate to extract urease from a podzol. Soil Biol. Biochem. 6:359-362.
  26. Nambiar, K.K.M. 1994. Soil fertility and Crop Productivity under Long-term Fertilizer use in India. Indian Council for agricultural research, New Delhi, India, pp. 27-28.
  27. Olsson, P.A., E. Baath, I. Jakobsen, and B. Soderstrom. 1995. The use of phospholipid and neutral lipid fatty acids to estimate biomass of arbuscular mycorrhizal fungi in soil. Mycol. Res. 99:623-629.
  28. NAAS. 2010. Fertilizer application recommendations for crop plants, National Academy of Agricultural Science, RDA, Suwon, Korea.
  29. Reichardt, W., G. Mascarina, B. Padre, and J. Doll. 1997. Microbial communities of continuously cropped, irrigated rice fields. Appl. Environ. Microbiol. 63:233-238.
  30. Ritchie, N.J., M.E. Schutter, R.P. Dick, and D.D. Myrold. 2000. Use of length heterogeneity-PCR and FAME to characterize microbial communities in soil. Appl. Environ. Microbiol. 66:1668-1675.
  31. Sasser, M. 1990. Identification of bacteria through fatty acid analysis. In: Klement, S., Rudolf, K., Sands, D., (Eds.), Methods in phytobacteriology. Akademiai Kiado, Budapest, pp. 199-204.
  32. Sarathchandra, S.U., K.W. Perrott, M.R. Boase, and J.E. Waller. 1988. Seasonal changes and the effects of fertiliser on some chemical, biochemical and microbiological characteristics of high-producing pastoral soil. Biol. Fertil. Soils. 6:328-335.
  33. Schjonning, P., S. Elmholt, L.J. Munkholm, K. Debosz. 2002. Soil quality aspects of humid sandy loams as influenced by organic and conventional long-term management. Agric. Ecosyst. Environ. 88:195-214.
  34. Schofield, R.K. 1949. Effect of pH on electric charges wried by clay particles. J. Soil Sci. 1:l-8.
  35. Schutter, M.E., and P.D. Richard. 2000. Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities. Soil Sci. Soc. Am. J. 64:1659-1668.
  36. Tabatabai, M.A. 1994. Soil enzymes. In: Weaver, R.W., Angel, J.S., Bottomley, P.S. (Eds.), Madison, Methods of soil analysis, part 2, Wisc., SSSA, pp. 775-833.
  37. Tabatabai, M.A. 1982. Assay of enzymes in soil. In: Page, A.L. (Ed.), Methods of Soil Analysis, Volume 2, American Society of Agronomy and Soil Science of America, Madison, WI, pp. 922-947.
  38. Torsvik, V., and D.F.L. Goksoyr. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
  39. Wander, M.M., D.S. Hedrick, D. Kaufman, S.J. Traina, B.R. Stinner, S.R. Kehrmeyer, and D.C. White. 1995. The functional significance of the microbial biomass in organic and conventionally managed soils. Plant and Soil. 170:87-97.
  40. Yadav, R.L., D.S. Yadav, R.M. Singh, and A. Kumar. 1998. Longterm effects of inorganic fertilizer inputs on crop productivity in a rice-wheat cropping system. Nutr. Cycl. Agroecosys. 51:193-200.