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Original Articles

Community Structure of Ammonia Oxidizing Bacteria and Their Potential to Produce Nitrous Oxide and Carbon Dioxide in Acid Tea Soils

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Pages 381-389 | Received 12 Dec 2007, Accepted 11 Jun 2008, Published online: 16 Oct 2008

REFERENCES

  • Ambus , P . 1998 . Nitrous oxide production by denitrification and nitrification in temperate forest, grassland and agricultural soil . Euro J Soil Sci , 49 : 495 – 502 .
  • Akiyama , H , Yan , X and Yagi , K . 2006 . Estimation of emission factors for fertilizer-induced direct N2O emission from agricultural soils in Japan: Summary of available data . Soil Sci Plant Nutr , 52 : 774 – 787 .
  • Allison , S M and Prosser , J I . 1991 . Urease activity in neutrophilic autotrophic ammonia oxidizing bacteria isolated from acid soils . Soil Biol Biochem , 23 : 45 – 51 .
  • Allison , S M and Prosser , J I . 1993 . Ammonia oxidation at low pH by attached populations of nitrifying bacteria . Soil Biol Biochem , 25 : 935 – 941 .
  • Anderson , J M and Ingram , J SI . 1989 . “ Colometric determination of ammonium ” . In Tropical Soil Biology and Fertility. ISSS , 42 – 43 . Wallingford, CT : CAB International .
  • Avrahami , S and Conrad , R . 2003 . Pattern of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperature . Appl Environ Microbiol , 69 : 6152 – 6164 .
  • Avrahami , S , Conrad , R and Braker , G . 2002 . Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers . Appl Environ Microbiol , 68 : 5685 – 5692 .
  • Backman , J SK , Hermansson , A , Tebbe , C C and Lindgren , P E . 2003 . Liming induces growth of a diverse flora of ammonia-oxidizing bacteria in acid spruce forest as determined by SSCP and DGGE . Soil Biol Biochem , 35 : 1337 – 1347 .
  • Backman , J SK , Klemedtsson , A , Klemedtsson , K L and Lindgren , P E . 2004 . Clear-cutting affects the ammonia oxidizer community differently in limed and non-limed coniferous forest soils . Biol Fertil Soils , 40 : 260 – 267 .
  • Barker , T , Bashmakov , I , Bernstein , L , Bogner , J E , Boch , P R , Dave , R O , Davidson , R , Fisher , B S , Gupta , S , Halsnæs , K , Heij , G J , Kahn Ribeiro , S , Kobayashi , S , Levine , M D , Martino , D L , Masera , O , Metz , B , Meyer , L A , Nabuurs , G J , Najam , A , Nakicenovic , N , Rogner , H H , Roy , J , Sathaye , J , Schock , R , Shukla , P , Sims , R EH , Smith , P , Tirpak , D A , Vorsatz , D U and Zhou , D . 2007 . “ Technical Summary ” . In : Climate Change 2007: Mitigation. Contribution of Working Group III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change , Edited by: Metz , B. , Davidson , O. R. , Bosch , P. R. , Dave , R. and Meyer , L. A. Cambridge, , United Kingdom and New York, USA : Cambridge University Press .
  • Berg , P , Klemedtsson , L and Rosswall , T . 1982 . Inhibitory effect of low partial pressures of acetylene on nitrification . Soil Biol Biochem , 14 : 301 – 303 .
  • Bollmann , A and Conrad , R . 1998 . Influence of O2 availability on NO and N2O release by nitrification and denitrification in soils . Global Change Biol , 4 : 387 – 396 .
  • Bouwman , A F . 1996 . Nitrogen oxides and tropical agriculture . Nature , 392 : 866 – 867 .
  • Bouwman , O T , Curtin , D , Cambell , C A , Biederbeck , V O and Ukrainetz , H . 1995 . Soil acidification from long-term use of anhydrous ammonium and urea . Soil Sci Soc Am J , 59 : 1488 – 1494 .
  • Burger , M and Jackson , L E . 2003 . Microbial immobilization of ammonium and nitrate in relation to ammonification and nitrification rates in organic and conventional cropping systems . Soil Biol Biochem , 35 : 29 – 36 .
  • Carney , K M , Matson , P A and Bohannan , B J . 2004 . Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land-use types . Ecol Lett , 7 : 684 – 694 .
  • Chu , H , Fujii , T , Morimoto , S , Lin , X , Yagi , K , Hu , J and Zhang , J . 2007 . Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a Sandy loam soil . Appl Environ Microbiol , 73 : 485 – 491 .
  • Conrad , R . 1996 . Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, N2O, and NO) . Microbiol Rev , 60 : 609 – 640 .
  • Davidson , E A , Matson , P A , Vitousek , P M , Riley , R , Dunklin , K , Garcia-Mendez , G and Maass , J M . 1993 . Processing regulating soil emission of NO and N2O in a seasonally dry tropical forest . Ecology , 74 : 130 – 130 .
  • De Boer , W and Kowalchuk , G A . 2001 . Nitrification in acid soils: microorganisms and mechanisms . Soil Biol Biochem , 33 : 853 – 866 .
  • Hadi , A , Jumadi , O , Inubushi , K and Yagi , K . 2008 . Mitigation options for N2O emission from a corn field in Kalimantan, Indonesia . Soil Sci Plant Nutr , 54 : 644 – 649 .
  • Hasting , R C , Butler , C , Singleton , I , Saunders , J R and McCarthy , A J . 2000 . Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation . Lett Appl Microbiol , 30 : 14 – 18 .
  • Hayashi , A , Sakamoto , K and Yoshida , T . 1997 . A rapid method for determination of nitrate in soil by hydrazine reduction procedure . Jpn J Soil Sci Plant Nutr , 68 : 322 – 326 . (in Japanese)
  • Hayatsu , M . 1993 . The lowest limit of pH for nitrification in tea soil and isolation of an acidophilic ammonia oxidizing bacterium . Soil Sci Plant Nutr , 39 : 219 – 226 .
  • Huang , Y , Zou , J , Zheng , X , Wang , Y and Xu , X . 2004 . Nitrous oxide emissions as influenced by amendment of plant residue with different C:N ratios . Soil Biol Biochem , 36 : 973 – 981 .
  • Inubushi , K , Naganuma , H and Kitahara , S . 1996 . Contribution of denitrification and autotrophic and heterotrophic nitrification to nitrous oxide production in andosols . Biol Fertil Soils , 23 : 292 – 298 .
  • Inubushi , K , Furukawa , Y , Hadi , A , Purnomo , E and Tsuruta , H . 2003 . Seasonal change of CO2, CH4 and N2O fluxes in relation to land-use change in tropical peatlands located in coastal area of South Kalimantan . Chemosphere , 52 : 603 – 608 .
  • Jordan , F L , Cantera , J J , Fenn , M E and Stein , L Y . 2005 . Autotrophic ammonia-oxidizing bacteria contribute minimally to nitrification in a nitrogen-impacted forested ecosystem . Appl Environ Microbiol , 71 : 197 – 206 .
  • Jumadi , O , Hala , Y and Inubushi , K . 2005 . Production and emission of nitrous oxide and responsible microorganisms in upland soil in Indonesia . Soil Sci Plant Nutr , 51 : 693 – 696 .
  • Jumadi , O , Hala , Y , Muis , A , Ali , A , Palennari , M , Yagi , K and Inubushi , K . 2008 . Influences of chemical fertilizers and a nitrification inhibitor on greenhouse gas fluxes in a Corn (Zea mays L.) field in Indonesia . Microbes Environ , 23 : 29 – 34 .
  • Kester , R A , Meijer , M E , Libochant , J A , Wietse , D B and Laanbroek , H J . 1997 . Contribution of nitrification and denitrification to the NO and N2O emissions of an acid forest acid, a river sediment and a fertilized grassland soil . Soil Biol Biochem , 29 : 1655 – 1664 .
  • Kowalchuk , G A and Stephen , J R . 2001 . Ammonia-oxidizing bacteria: a model for molecular microbial ecology . Annu Rev Microbiol , 55 : 485 – 529 .
  • Kowalchuk , G A , Stienstra , A W , Heilig , G H , Stephen , J R and Woldendorp , J W . 2000 . Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche (The Netherlands) . FEMS Microbiol Ecol , 31 : 207 – 215 .
  • Kramer , A W , Doane , T A , Horwath , W R and van Kessel , C . 2002 . Combining fertilizer and organic inputs to synchronize N supply in alternative cropping system in California . Agric Ecosyst Environ , 34 : 43 – 50 .
  • Laverman , A M , Speksnijder , A GCL , Braster , M , Kowalchuk , G A , Verhoef , H A and van Verseveld , H W . 2001 . Spatiotemporal stability of an ammonia-oxidizing community in an N saturated forest soil . Microbiol Ecol , 42 : 35 – 45 .
  • Nicolaisen , M H and Ramsing , N B . 2002 . Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria . J Microbiol Meth , 50 : 189 – 203 .
  • Nioh , I , Isobe , T and Osada , M . 1993 . Microbial biomass and same biochemical characteristics of a strongly acid tea field soil . Soil Sci Plant Nutr , 39 : 617 – 626 .
  • Nugroho , R A , Roling , W FM , Laverman , A M , Zoomer , H R and Verhof , H A . 2005 . Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils . FEMS Microbiol Ecol , 53 : 473 – 481 .
  • Oh , K , Kato , T , Li , Z P and Li , F Y . 2006 . Environment problems from tea cultivation in Japan and a control measure using calcium cyanamide . Pedosphere , 16 : 770 – 777 .
  • Poth , M and Focht , D D . 1985 . 15N kinetic analysis of N2O production by Nitrosomonas europeae: An examination of nitrifier denitrification . Appl Environ Microbiol , 49 : 1134 – 1141 .
  • Recous , S , Mary , B and Faurie , G . 1990 . Microbial immobilization of ammonium and nitrate in cultivated soils . Soil Biol Biochem , 22 : 913 – 922 .
  • Robertson , G P and Tiedje , J M . 1987 . Nitrous oxide source in aerobic soils: Nitrification, denitrification and other biological processes . Soil Biol Biochem , 19 : 187 – 193 .
  • Rotthauwe , J H , Witzel , K P and Liesack , W . 1997 . The ammonium monooxidase structural gene amoA as a functional marker: molecular fine scale analysis of natural ammonium-oxidizing population . Appl Environ Microbiol , 63 : 4704 – 4712 .
  • Schmidt , C S , Hultman , K A , Robinson , D , Killham , K and Prosser , J I . 2007 . PCR profiling of ammonium-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition . FEMS Microbiol Ecol , 61 : 305 – 316 .
  • Stephen , J R , McCaig , A E , Smith , Z , Prosser , J I and Embley , T M . 1996 . Molecular diversity of soil and marine 16S rRNA gene sequences related to B-subgroup ammonia-oxidizing bacteria . Appl Environ Microbiol , 62 : 4147 – 4154 .
  • Tamura , K , Dudley , J , Nei , M and Kumar , S . 2007 . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 . Molecular Biol Evol , 24 : 1596 – 1599 .
  • Tokuda , S and Hayatsu , M . 2000 . Nitrous oxide production from strong acid tea field soils . Soil Sci Plant Nutr , 46 : 835 – 844 .
  • Tokuda , S and Hayatsu , M . 2001 . Nitrous oxide emission potential of 21 acidic tea field soils in Japan . Soil Sci Plant Nutr , 47 : 637 – 642 .
  • Zaman , M , Matsushima , M , Chang , S X , Inubushi , K , Nguyen , L , Goto , S , Kaneko , F and Yoneyama , T . 2004 . Nitrogen mineralization, N2O production and soil microbiological properties as affected by long-term applications of sewage sludge composts . Biol Fertil Soils , 40 : 101 – 109 .
  • Wang , X J , Hu , X F and Chen , H Z . 1997 . Some biogeochemical characteristic of tea soils . Pedosphere , 7 : 275 – 280 .

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