Role of microbial biomass in biogeochemical processes in paddy soil environments

Soil Science and Plant Nutrition

Volumn 50, Issue 6, 2004, Pages 793-805

  Inubushi, Kazuyuki ^a   Acquaye, Solomon ^a,b  

^a CHIBA UNIVERSITY   (Japan)

^b Ghana Irrigation Authority   (Ghana)

Author keywords

Biogeochemical processes; Nutrient cycling; Paddy soil ecosystem; Soil microbial biomass; Soil microbial biomass measurement

Indexed keywords

BACTERIA (MICROORGANISMS); FUNGI; PROTOZOA;

EID: 11144294192     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1080/00380768.2004.10408539     Document Type: Article

References (107)

1. Acquaye S 2003: Effects of N fertilization, soil type and elevated carbon dioxide concentration on changes in the soil microbial biomass in flooded-rice and upland agroecosystems. PhD Thesis. Graduate School of Science and Technology, Chiba University
2. Acquaye S, Hadi A, Cheng W, and lnubushi K 2000: Effect of fertilizers on soil microbial biomass in two types of paddy fields. The Technical Bulletin, Faculty of Horticulture, Chiha Uniersity, 54, 1-10
3. Acquaye S and Tnubushi K 2004: Comparative effects of coated and non-coated urea in clayey and sandy paddy soil microcosms examined by the 15N tracer technique. II. Effects on soil microbial biomass N and microbial 15N immobilization. Soil Sci. Plant Nutr., 50, 215-223
4. Amato M and Ladel JN 1988: Assay for microbial biomass based on ninhydrin-reactive nitrogen in extracts of fumigated soil. Soil Bioi. Biochem., 20, 107-114
5. Amato M and Ladd JN 1992: Decomposition of '4C-labeled glucose and legume material in soils: properties influencing the accumulation of organic residues C and microbial biomass C. Soil Bioi. Biochem., 24, 455-464
6. Anthony C 1986: Bacterial oxidation of methane and methanol. Adv. Microh. Physiol., 27, 113-210
7. Baath E, Diaz-Ravina M, Frostegard A, and Campbell C 1998: Effect of metal-rich sludge amendments on the soil microbial community. Appl. Environ. Microbial., 64, 238-245
8. Bailey VL, Peacock AD, Smith JL, and Bolton Jr H 2002: Relationship between soil microbial biomass detennined by chloroform fumigation-extraction, substrate induced respiration, and phospholipid fatty acid analysis. Soil Bioi. Biochem., 34, 1385-1389
9. Baird BH and White DC 1985: Biomass and community structure of the abyssal microbiota determined from basin and Puerto Rico trench sediments. In Benthic Ecology and Sedimentary Processes of Venezuela Basin-Past and Present, Vol. 61, Ed. DK Young and MD Richardson, p. 217-223, Elsevier, Amsterdam
10. Barak P, Molina JAE, Hadas A, and Clapp CE 1990: Mineralization of amino acids and evidence uf direct assimilation of organic nitrogen. Soil Sci. Soc. Am. J., 54, 769-774
11. Bardgett RD, Hobbs PJ, and Frostegard A 1996: Changes in soil fungal: Bacterial biomass ratios following reductions in the intensity of management of an upland grassland. Bioi. Fertil. Soils, 22, 261-264
12. Bloem J, Bolhuis PR, Veninga MR, and Wieringa J 1995: Microscopic methods for counting bacteria and fungi in soil. In Methods in Applied Microbiology and Biochemistry, Ed. K Alef and P Nannipieri, p. 162-175, Academic Press, London
13. Bornemann JP, Skroch W, O'Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhus J, and Triplet EW 1996: Molecular microbial diversity of an aglicultural soil in Wisconsin. Appl. Environ. Microhiol., 62, 1935-1943
14. Bossio D and Scow DM 1998: Impact of carbon and flooding on soil microbial communities: Phospholipid fatty acid profiles and substrate utilization patterns. Appl. Environ. MiCI•obiol., 61, 4043-5050
15. Broadbent FE and Nakashima T 1970: Nitrogen immobilization in flooded soils. Soil Sci Soc. Am. Proc., 34, 218-221
16. Brookes PC and McGrath SP 1984: The effect of metal toxicity on the soil microbial biomass. J. Soil Sci., 35, 341-346
17. Brookes PC, Powlson DS, and Jenkinson DS 1982: Measurement of microbial biomass phosphorus in soil. Soil Bioi. Biochem., 14. 319-329
18. Bums RG 1978: Enzyme activity in soil: Some theoretical and practical considerations. In Soil Enzymes, Ed. RG Bums, p. 295-340, Academic Press, New York
19. Cabrera ML and Beare MH 1993: Alkaline persulphate oxidation for detennining total nitrogen in microbial extracts. Soil Sci. Soc. Am. J., 57, 1007-1012
20. Carreres R, Gonzales Tom R, Sendra J, Ballesteros R, Villiante EF, Quesada A, Nieva M, and Leganes F 1996: Effect of nitrogen rate on rice growth and biological nitrogen fixation. J. Agric. Sci., 127, 295-302
21. Cavigelli MA, Robertson GP, and Klug MJ 1995: Fatty acid methyl esters (FAME) profiles as measures of soil microbial community structure. Plant Soil, 170, 99-113
22. 2 and temperature on microbial biomass nitrogen and nitrogen mineralization in submerged soil microcosms. Soil Microorg., 54, 51-59
23. FleiBbach A, Mader P, and Niggli U 2000: Mineralization and microbial assimilation uf 14C-labeled straw in soils of organic and conventional agricultural systems. Soil Bioi. Biochem., 32, 1131-1139
24. Frostegard A and Baath E 1996: The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in suil. Bioi. Fertil. Soils, 22, 59-65
25. Frostegard A, Tunlid A, and Baath E 1996: Changes in microbial community structure during long-te1m incubation in two soils experimentally contaminated with metals. Soil Bioi. Biochem., 28, 55-63
26. Fry JC 1990: Direct methods and biomass estimation. In Methods in Microbiology, Vol. 22, Techniques in Microbial Ecology, Ed. R Grigorova and JR Noitios, p. 41-85, Academic Press, London
27. Gaunt JL, Neue HU, Cassman KG, Olk DC, Arah JRM, Witts C, Ottow JCG, and Grant IF 1995: Microbial biomass and organic matter turnover in wetland rice soils. Bioi. Fertil. Soils, 19, 333-342
28. Gray TRG 1990: Methods for studying microbial ecology in soil. In Methods in Microbiology, Vol. 22, Techniques in microbial ecology, Ed. R Grigorova and JR NmTios, p. 309-342, Academic Press, London
29. Hasebe A, Kanasawa S, and Takai Y 1985: Microbial biomass in paddy soil. Il. Microbial biomass carbon measured by Jenkinson's fumigation method. Soil Sci. Plant Nutr., 31, 349-359
30. 2 enrichment (FACE) at three levels of nitrogen fertilization in a paddy field. Bioi. Fertil. Soils, 34, 453-459
31. Inubushi K, Acquaye S, Tsukagoshi S, Shibahara F, and Komatsu S 2002: Effects of controlled-release coated urea (CRCU) on soil microbial biomass N in paddy fields examined by the 15N tracer technique. Nutr. Cycl. Agroecosyst., 63,291-300
32. Inubushi K, Brookes PC, and Jenkinson DS 1989a: Influence of paraquat on the extraction of adenosine triphosphate from soil by trichloroacetic acid. Soil Bioi. Biochem., 21, 741-742
33. Inubushi K, Brookes PC, and Jenkinson OS 1991: Soil microbial biomass C, N and ninhydrin-N in aerobic and anaerobic soils measured by the fumigation-extraction method. Soil Bioi. Biochem., 23, 737-741
34. 2 and temperature. Soil Sci. Plant Nutr., 45, 863-872
35. 2 emichment (FACE) on microbial biomass in paddy soil. Soil Sci. Plant Nutr., 47, 737-745
36. Inubushi K, Hori K, Matsumoto S, Umebayashi M, and Wada H 1989b: Methane emission from the flooded rice soil to the atmosphere through rice plant Ipn. J. Soil Sci. Plant Nutr., 60, 318-324
37. Inubushi K, Shibahara F, Hasegawa K, and Yamamuro S 1997: Effects of added organic matter on microbial biomass nitrogen dynamics and plant uptake in paddy soils. In Plant Nutrition for Sustainable Food Production and Environment, Ed. T Ando et al., p. 777-778, Kluwer Academic Publishers, Netherlands
38. Inubushi K, Wada H, and Takai Y 1984a: Easily decomposable organic matter in paddy soils (IV): Relationship between reduction process and organic matter decomposition. Soil Sci. Plant Nutr., 30, 189-198
39. Inubushi K, Wada H, and Takai Y 1984b: Determination of microbial biomass nitrogen in submerged soils. Soil Sci. Plant Nutr., 30, 455-459
40. Inubushi K, Wada H, and Takai Y 1985: Factors influencing the determination of microbial biomass nitrogen in submerged soils. Soil Sci. Plant Nutr., 31,481-485
41. Inubushi K and Watanabe I 1986: Dynamics of available nitrogen in paddy soils: II. Mineralized N of chlorofonn-fumigated soil as a nutrient source for rice. Soil Sci Plant Nutr., 32, 561-577
42. Jenkinson DS 1966: Studies on the decomposition of plant material in soil. II. Partial sterilization of soil and the soil biomass. J. Soil Sci., 17, 280-302
43. Jenkinson OS and Ladd JN 1981: Microbial biomass in soil: measurement and turnover. In Soil Biochemistry 5, Ed. EA Paul and JN Ladd, p. 415-471, Marcel Dekker, New York
44. Jenkinson DS and Powlson DS 1976: The effect of biocidal treatments on metabolism in soil (V)-A method for measuring soil biomass. Soil Bioi. Biochem., 8, 209-213
45. Joergensen RG and Brookes PC 1990: Ninhydrin-reactive nitrogen measurements of microbial biomass in 0.5 M K2S04 soil extracts. Soil Bioi. Biochem., 22, 1023-1027
46. Kennedy AC 1994: Carbon utilization and fatty acid profiles for characterization of bacteria. In Methods of Soil Analysis Part 2. Microbiological and Biochemical Properties, p. 543-556, Soil Science Society of America, Madison, Wisconsin
47. Killham 1994: Soil redox potential. In Soil Ecology, p. 20-24, Cambridge University Press, Cambridge, UK
48. King AW, Emmanuel WR, and Post WM 1992: Projecting future concentrations of atmospheric CO, with global carbon cycle models: the importance of simulating histmical changes. Environ. Manag., 16, 91-108
49. 2 exchange at the floodwater-water surface in a rice paddy field. New Phytol., 150, 231-239
50. Kozdroj J and van Elsas JD 2001: Structural diversity of microbial communities in arable soils of a heavily industrialized area determined by PCR-DGGE fingerptinting and FAME profiling. Appl. Soil Ecol., 17, 31-42
51. Kyuma K 1989: Rice soils of Asia: distiibution and management. In Classification and Management of Rice Growing Soils, Ed. BP Jan. Proceedings of the Fifth International Soil Management Workshop, 11-23 Dec 1988, p.l5-27, Taichung, Taiwan
52. Ladd JN 1978: Origin and range of enzyme in soil. In Soil Enzyme, Ed. RG Bums, p. 51-96, Academic Press, New York
53. Ladd JN, Amato M, Grace PR, and van Veen JA 1995: Simulation of 14C turnover through the microbial biomass in soils incubated with 14C-labelled plant residue. Soil Bioi. Biochem., 27, 777-783
54. Lynch JM 1983: Soil Biotechnology, Blackwell Sci. Publications, p. 91, Oxford, England
55. McLatchey GP and Reddy KR 1998: Regulation of organic matter decomposition and nutrient release in wetland soil. J. Environ. Qual., 27, 1268-1274
56. Miyama S 1990: Fertilizer application to rice based on the optimum amount of N in the plant and patterns of soil N uptake by rice. In Nitrogen Mineralization in Paddy Soils and Fertilizer Application to Rice, Ed. S Sekiya and T Yoshino, p. 63-97, Hakuyusha, Tokyo
57. Montealegre CM, van Kessel C, Russel MP, and Sadowsky M 2002: Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide. Plant Soil, 243, 197-207
58. 2O Global Emissions and Controls from Rice fields and other Agricultural and Industrial Sources-NIAES series 2, Eel. K Minami, A Mossier, and R Sass, p. 135-139, NIAES, Tsukuba, Japan
59. Mulvaney RL 1991: Some recent advances in the use of 15N for research in nitrogen transformations in soil. Proceedings of Symposium on Stable Isotopes in Plant Nutrition, Soil Fertility and Environmental Studies. IAEA, Vienna 1-5 Oct., p. 283-296
60. Muyzer G, de Waal EC, and Uitterlinden A 1993: Profiling of complex microbial populations using denaturing gel gradient electrophoresis analysis of polymerase chain reactionamplified genes coding for 16s rRNA. Appl. Environ. Microbioi., 59, 695-700
61. Myrold DD and Tiedje JM 1986: Simultaneous estimation of several nitrogen cycle rates using 15N: Theory and application. Soil Bioi. Biochem., 18, 559-568
62. Niemi RM, Heiskanen I, Wallenius K, and Lindstrom K 2001: Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consm1ia. J. Microbial. Meth., 45, 155-165
63. + dilution technique. Soil Bioi. Biochem., 17, 149-154
64. Niswati A, Yamazaki M, Jkenaga M, and Kimura M 2002: Bacterial communities associated with aquatic organisms in the floodwater of a Japanese paddy field estimated by RFLP pattern analysis. Soil Sci. Plant Nutr., 48, 185-193
65. Nouchi I, Mariko S, and Aoki K 1990: Mechanism of methane transportation from the rhizosphere to the atmosphere through rice plant. Plant Physiol., 94, 59-66
66. Okabe A, Oike H, Toyota A, and Kimura M 2000a: Seasonal variations of phospholipid fatty acid composition in the floodwater of a Japanese paddy field under a long-term fertilizer trial. Soil Sci Plant Nutr., 46, 177-188
67. Okabe A, Oike H, Toyota A, and Kimura M 2000b: Compa1ison of phospholipid fatty acid composition in the floodwater and plow layer soil during the rice cultivation period in a Japanese paddy soil. Soil Sci Plant Nutr., 46, 893-904
68. Pennanen T, Frostegard A, Fritze H, and BiHith E 1996: Phospholipid fatty acid composition and heavy metal tolerance of soil microbial communities along two heavy metal-polluted gradients in coniferous forests. Appl. Environ. Microhiol., 62, 420-428
69. Powlson DS 1994: The soil microbial biomass: before, beyond and back. In Beyond the Biomass, Ed. K Ritz, J Dighton, and KE Giller, p. 3-20, John Wiley and Sons, Chichester
70. Powlson DS, Brookes PC, and Christensen BT 1987: Measurement of soil microbial biomass provides an early indication of changes in total soil organic matter due to straw incorporation. Soil Bioi. Biochenz., 19, 159-164
71. Reichardt W, Briones A, Padre B, de Jesus R, and Mascarina G 1996: Dynamics of soil microbial communities and sustainable nutrient supply in highly intensified rice cultivation. Proceedings of International Symposium on Maximizing Sustainable Rice Yields through Improved Soil and Environmental Management, Thailand, Vol. 2, p. 887-896
72. Reichardt W, lnubushi K, and Tiedje J 2000: Microbial processes in C and N dynamics. In Carbon and Nitrogen Dynamics in Flooded Soils, Ed. GJD Kirk and DC Olk, p. 101-146, IRRI, Los Banos, Philippines
73. Reichardt W, Mascarina G, Padre B, and Doll L 1997: Microbial communities of continuously cropped in•igated rice fields. Appl. Environ. Microbiol., 63, 233-238
74. Ringelberg DB, Stair JO, Almeida J, Norby RJ, O'Neil EG, and White DC 1997: Consequences of rising atmospheric carbon dioxide level for the below ground microbiota associated with white oak. J. Environ. Qual., 26, 495-503
75. Roger PA and Ladha JK 1992: Biological N2-fixation in wetland rice fields: estimation and contribution to nitrogen balance. Plant Soil, 141, 41-55
76. Saggar S, Bettany JR, and Stewart JWB 1981: Measurement of microbial sulphur in soil. Soil Bioi. Biochem., 13, 493-498
77. Saito M and Watanabe I 1978: Organic matter production in rice field floodwater. Soil Sci. Plant Nutr., 24, 427-440
78. 4 and Np Global Emissions and Controls from Rice Fields and Other Agricultural and Industrial Sources-NIAES series 2, Ed. K Minami, AR Mossier, and R Sass, p. 1-7, NIAES, Tsukuba, Japan
79. Sethunathan N, Rao VR, Adhya TK, and Raghu K 1983: Microbiology of Rice Soils. CRC Crit. Rev. Microbial., 10, 125-172
80. Sakamoto K and Hodono N 2000: Tumover time of microbial biomass carbon in Japanese upland soils with different textures. Soil Sci. Plant Nutr., 46, 483-490
81. Shibahara F and Inubushi K 1995: Measurement of microbial biomass C and N in paddy soils by the fumigation-extraction method. Soil Sci. Plant Nutr., 41, 681-689
82. Shibahara F and lnubushi K 1997: Effects of organic matter application on microbial biomass and available nutrients in vmious types of paddy soils. Soil Sci. Plant Nutr., 43, 191-203
83. Shibahara F, Yamamuro S, and Inubushi K 1998: Dynamics of microbial biomass nitrogen as influenced by organic matter application in paddy soils: I. Fate of fertilizer and soil organic N detennined by 15N tracer technique. Soil Sci. Plant Nutr., 44, 167-178
84. Shimidzu M, Nakajima Y, Matsuya K, and Kimura M 2002: Comparison of phospholipid fatty acid composition in percolating water, floodwater, and the plow layer soil during rice cultivation period in Japanese paddy fields. Soil Sci. Plant Nutr., 48, 595-600
85. Shoji S and Gandenza AT 1992: Controlled Release Fertilizers with Polyolefin Resin Coating: Development, Properties and Utilization, Ed. S Shoji and AT Gandenza, p. 63-75, Konno Printing Co., Sendai, Japan
86. Sparling GP 1992: Ratio of microbial biomass carbon to soil organic carbon as a sensitive indicator of changes m soil organic matter. Aust. J. Soil Res., 30, 195-207
87. Steinberger Y, Zelles L, Bai QY, von Lutow M, and Munch JC 1999: Phospholipid acid profiles as indicators for the microbial community structure in soils along a climatic transect in the Judean desert. Bioi. Fertil. Soils, 28, 292-300
88. Stockdale EA and Rees RM 1994: Relationship between biomass nitrogen and nitrogen extracted by other nitrogen available methods. Soil Bioi. Biochem. 213, 1213-1220
89. Talley SN, Talley BJ, and Rains DW 1977: Nitrogen fixation by kolla in rice fields. In Genetic Engineering for Nitrogen Fixation, Ed. A Hollaender et al., p. 259-281, Plenum Press, New York and London
90. Toor GS and Beri V 1991: Extent of fertilizer-N immobilized by the application of rice straw and its availability in soils. Bioresour. Tech., 37, 189-191
91. Tun CC, lkenaga M, Asakawa S, and Kimura M 2002: Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis. Soil Sci. Plant Nutr., 48, 805-813
92. Tunlid A and White DC 1992: Biochemical analysis of biomass, community structure, nutritional status and metabolic activity of microbial communities in soil. In Soil Biochemistry (No.7), Ed. G Stotzky and J-M Bollag, p. 229-262, Marcel Dekker, New York
93. Ueno H and Yamamuro S 1997: N dynamics in paper-mulched paddy field fe11ilized with controlled-release coated urea by 1'N method. In Plant Nutrition for Sustainable Food Production and Environment, Ed. T Ando et al., p. 539-540, Kluwer Academic Publishers, Japan
94. 4 under different moisture regimes. Soil Bioi. Biochem., 17, 257-274
95. Vance ED, Brookes PC, and Jenkinson DS 1987: An extraction method for measuring soil microbial biomass C. Soil Bioi. Biochem., 22, 703-707
96. Vestal JR and White DC 1989: Lipid analysis in microbial ecology-Quantitative approaches to the study of microbial communities. Bio. Science, 39, 535-541
97. Vlek PLG and Craswell ET 1981: Ammonia volatilization from flooded soils. Fertil. Res., 2, 227-245
98. Watanabe I and Furusaka C 1980: Microbial ecology of flooded rice soils. Adv. Microb. Ecol., 4, 125-167
99. Watanabe I and Inubushi K 1986: Dynamics of available nitrogen in paddy soils: I. Changes in available N during rice cultivation and origin of N. Soil Sci. Plant Nutr., 32, 37-50
100. White DC, Davis WM, Nickels JS, King JD, and Robbie RJ 1979: Detem1ination of sedimentary microbial biomass by extractable lipid phosphate. Oecoloflia, 40, 51-62
101. Wu J, Joergensen RG, Pommerening B, Chaussod R, and Brookes PC 1990: Measurement of soil microbial biomass C by fumigation-extractionAn automated procedure. Soil Bioi. Biochem., 22, 1167-1169
102. Yamagishi T, Watanabe J, Okada K, Hayashi T, Kumura A, and Murata Y 1980: Cycling of C in paddy field. II. Biomass and gross production of algae. Jpn. J. Crop Sci., 49, 146-155
103. 2. Ecol. Appl., 61, 257-262
104. Zelles L 1988: The simultaneous detennination of muramic acid and glucosamine in soil by high-performance liquid chromatography with pre-column fluorescence derivatization. Bioi. Fertil. Soil, 6, 125-130
105. Zelles L, Adrian P, Bai QY, Stepper K, Adrian MY, Fischer K, Maier A, and Ziegler A 1991: Microbial activity measured in soils stored under different temperature and humidity conditions. Soil Bioi. Biochem., 24, 317-323
106. Zelles L, Bai QY, Beck T, and Beese F 1992: Signature fatty acids in the phospholipids and 1ipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Bioi. Biochem., 24, 317-323
107. Zelles L, Bai QY, Mai RX, Rackwitz R, Winter K, and Beese F 1994: Microbial biomass, metabolic activity and nutritional status determined from fatty acid patterns and poly-hydroxybutyrate in agriculturally managed soils. Soil Bioi. Biochem., 26, 439-446