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Volumn 24, Issue 2, 2009, Pages 168-174

Analysis of ammonia monooxygenase and archaeal 16S rRNA gene fragments in nitrifying acid-sulfate soil microcosms

Author keywords

Acid sulfate soil; Ammonia oxidizing archaea; Ammonia oxidizing bacteria; Low pH; Nitrification

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; NITROSOMONADALES; NITROSOSPIRA;

EID: 70349995572     PISSN: 13426311     EISSN: 13426311     Source Type: Journal    
DOI: 10.1264/jsme2.ME09104     Document Type: Article
Times cited : (18)

References (54)
  • 1
    • 0002367729 scopus 로고    scopus 로고
    • MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
    • Adachi, J., and M. Hasegawa. 1996. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.
    • (1996) Comput. Sci. Monogr. , vol.28 , pp. 1-150
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 51349088322 scopus 로고    scopus 로고
    • Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of Northern Arizona, USA
    • Adair, K.L., and E. Schwartz. 2008. Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of Northern Arizona, USA. Microb. Ecol. 56:420-426.
    • (2008) Microb. Ecol. , vol.56 , pp. 420-426
    • Adair, K.L.1    Schwartz, E.2
  • 3
    • 0000340101 scopus 로고
    • Identification of heterotrophic nitrification in strongly acid larch humus
    • Adams, J. A. 1986. Identification of heterotrophic nitrification in strongly acid larch humus. Soil Biol. Biochem. 18:339-341.
    • (1986) Soil Biol. Biochem , vol.18 , pp. 339-341
    • Adams, J.A.1
  • 4
    • 0002548207 scopus 로고
    • Ammonia oxidation at low pH by attached populations of nitrifying bacteria
    • Allison, S. M., and J. I. Prosser. 1993. Ammonia oxidation at low pH by attached populations of nitrifying bacteria. Soil Biol. Biochem. 25:935-941.
    • (1993) Soil Biol. Biochem , vol.25 , pp. 935-941
    • Allison, S.M.1    Prosser, J.I.2
  • 6
    • 0000027201 scopus 로고
    • Production of nitrous oxide by ammonia-oxidizing chemoautotrophic microorganisms in soil
    • Blackmer, A. M., J. M. Bremner, and E. L. Schmidt. 1980. Production of nitrous oxide by ammonia-oxidizing chemoautotrophic microorganisms in soil. Appl. Environ. Microbiol. 40:1060-1066.
    • (1980) Appl. Environ. Microbiol , vol.40 , pp. 1060-1066
    • Blackmer, A.M.1    Bremner, J.M.2    Schmidt, E.L.3
  • 7
    • 0035408582 scopus 로고    scopus 로고
    • Autotrophic ammonia oxidation at low pH through urea hydrolysis
    • Burton, S. A. Q., and J. I. Prosser. 2001. Autotrophic ammonia oxidation at low pH through urea hydrolysis. Appl. Environ. Microbiol. 67:2952-2957.
    • (2001) Appl. Environ. Microbiol , vol.67 , pp. 2952-2957
    • Burton, S.A.Q.1    Prosser, J.I.2
  • 8
    • 0024164999 scopus 로고
    • Autotrophic nitrification in a fertilized acid heath soil
    • de Boer, W., H. Duyts, and H. J. Laanbroek. 1988. Autotrophic nitrification in a fertilized acid heath soil. Soil Biol. Biochem. 20:845-850.
    • (1988) Soil Biol. Biochem , vol.20 , pp. 845-850
    • De Boer, W.1    Duyts, H.2    Laanbroek, H.J.3
  • 10
  • 11
    • 0029473277 scopus 로고
    • A world perspective on acid sulphate soils
    • Dent, D. L., and L. J. Pons. 1995. A world perspective on acid sulphate soils. Geoderma 67:263-276.
    • (1995) Geoderma , vol.67 , pp. 263-276
    • Dent, D.L.1    Pons, L.J.2
  • 12
    • 26844541457 scopus 로고    scopus 로고
    • Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
    • Francis, C. A., K. J. Roberts, J. M. Beman, A. E. Santoro, and B. B. Oakley. 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. USA 102:14683-14688.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 14683-14688
    • Francis, C.A.1    Roberts, K.J.2    Beman, J.M.3    Santoro, A.E.4    Oakley, B.B.5
  • 13
    • 33745170356 scopus 로고    scopus 로고
    • Nitrification in a biofilm at low pH values: Role of in situ microenvironments and acid tolerance
    • Gieseke, A., S. Tarre, M. Green, and D. de Beer. 2006. Nitrification in a biofilm at low pH values: Role of in situ microenvironments and acid tolerance. Appl. Environ. Microbiol. 72:4283-4292.
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 4283-4292
    • Gieseke, A.1    Tarre, S.2    Green, M.3    De Beer, D.4
  • 14
    • 40549127742 scopus 로고    scopus 로고
    • Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile
    • Hansel, C. M., S. Fendorf, P. M. Jardine, and C. A. Francis. 2008. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microbiol. 74:1620-1633.
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 1620-1633
    • Hansel, C.M.1    Fendorf, S.2    Jardine, P.M.3    Francis, C.A.4
  • 16
    • 84951581596 scopus 로고
    • The lowest limit of pH for nitrification in tea soil and isolation of an acidophilic ammonia oxidizing bacterium
    • 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.
    • (1993) Soil Sci. Plant Nutr , vol.39 , pp. 219-226
    • Hayatsu, M.1
  • 17
    • 34547686149 scopus 로고    scopus 로고
    • Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices
    • He, J. -Z, J. -P. Shen, L. -M. Zhang, Y. -G. Zhu, Y. -M. Zheng, M. -G. Xu, and H. Di. 2007. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ. Microbiol. 9:2364-2374.
    • (2007) Environ. Microbiol. , vol.9 , pp. 2364-2374
    • He, J.-Z.1    Shen, -P.J.2    Zhang, -M.L.3    Zhu, -G.Y.4    Zheng, -M.Y.5    Xu, -G.M.6    Di, H.7
  • 18
    • 0030894624 scopus 로고    scopus 로고
    • Novel group within the kingdom Crenarchaeota from boreal forest soil
    • Jurgens, G., K. Lindstrom, and A. Saano. 1997. Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63:803-805.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 803-805
    • Jurgens, G.1    Lindstrom, K.2    Saano, A.3
  • 19
    • 0002888487 scopus 로고
    • Short-term assay of soil urease activity using colorimetric determination of ammonium
    • Kandeler, E., and H. Gerber. 1988. Short-term assay of soil urease activity using colorimetric determination of ammonium. Biol. Fertil. Soils 6:68-72.
    • (1988) Biol. Fertil. Soils. , vol.6 , pp. 68-72
    • Kandeler, E.1    Gerber, H.2
  • 21
    • 34249106390 scopus 로고    scopus 로고
    • High abundance of Crenarchaeota in a temperate acidic forest soil
    • Kemnitz, D., S. Kolb, and R. Conrad. 2007. High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol. Ecol. 60:442-448.
    • (2007) FEMS Microbiol. Ecol. , vol.60 , pp. 442-448
    • Kemnitz, D.1    Kolb, S.2    Conrad, R.3
  • 23
    • 0034548634 scopus 로고    scopus 로고
    • Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands
    • Kowalchuk, G. A., A. W. Stienstra, G. H. J. Heilig, J. R. Stephen, and J. W. Woldendorp. 2000. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ. Microbiol. 2:99-110.
    • (2000) Environ. Microbiol. , vol.2 , pp. 99-110
    • Kowalchuk, G.A.1    Stienstra, A.W.2    Heilig, G.H.J.3    Stephen, J.R.4    Woldendorp, J.W.5
  • 27
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman, D. J., and W. R. Pearson. 1985. Rapid and sensitive protein similarity searches. Science 227:1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 28
    • 0022230522 scopus 로고
    • Nitrification in forest soil of different pH as affected by urea, ammonium sulphate and potassium sulphate
    • Martikainen, P. J. 1985. Nitrification in forest soil of different pH as affected by urea, ammonium sulphate and potassium sulphate. Soil Biol. Biochem. 17:363-367.
    • (1985) Soil Biol. Biochem. , vol.17 , pp. 363-367
    • Martikainen, P.J.1
  • 29
    • 34248562051 scopus 로고    scopus 로고
    • 2O product ratio of nitrification and its dependence on long-term changes in soil pH
    • Moørkved, P. T., P. Dörsch, and L. R. Bakken. 2007. The N2O product ratio of nitrification and its dependence on long-term changes in soil pH. Soil Biol. Biochem. 39:2048-2057.
    • (2007) Soil Biol. Biochem. , vol.39 , pp. 2048-2057
    • Moørkved, P.T.1    Dörsch, P.2    Bakken, L.R.3
  • 31
    • 33745792553 scopus 로고    scopus 로고
    • Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation
    • Nicol, G. W., D. Tscherko, L. Chang, U. Hammesfahr, and J. I. Prosser. 2006. Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation. Environ. Microbiol. 8:1382-1393.
    • (2006) Environ. Microbiol , vol.8 , pp. 1382-1393
    • Nicol, G.W.1    Tscherko, D.2    Chang, L.3    Hammesfahr, U.4    Prosser, J.I.5
  • 32
    • 33947221558 scopus 로고    scopus 로고
    • Afforestation of moorland leads to changes in crenarchaeal community structure
    • Nicol, G. W., C. D. Campbell, S. J. Chapman, and J. I. Prosser. 2007. Afforestation of moorland leads to changes in crenarchaeal community structure. FEMS Microbiol. Ecol. 60:51-59.
    • (2007) FEMS Microbiol. Ecol. , vol.60 , pp. 51-59
    • Nicol, G.W.1    Campbell, C.D.2    Chapman, S.J.3    Prosser, J.I.4
  • 33
    • 52949137846 scopus 로고    scopus 로고
    • The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria
    • Nicol, G. W., S. Leininger, C. Schleper, and J. I. Prosser. 2008. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ. Microbiol. 10:2966-2978.
    • (2008) Environ. Microbiol. , vol.10 , pp. 2966-2978
    • Nicol, G.W.1    Leininger, S.2    Schleper, C.3    Prosser, J.I.4
  • 34
    • 70349928983 scopus 로고    scopus 로고
    • Archaeal diversity of upland rice field soils assessed by the terminal restriction fragment length polymorphism method combined with real time quantitative-PCR and a clone library analysis
    • Nishizawa, T., M. Komatsuzaki, N. Kaneko, and H. Ohta. 2008. Archaeal diversity of upland rice field soils assessed by the terminal restriction fragment length polymorphism method combined with real time quantitative-PCR and a clone library analysis. Microbes Environ. 23:237-243.
    • (2008) Microbes Environ. , vol.23 , pp. 237-243
    • Nishizawa, T.1    Komatsuzaki, M.2    Kaneko, N.3    Ohta, H.4
  • 35
    • 0042853314 scopus 로고    scopus 로고
    • Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR
    • Ochsenreiter, T., D. Selezi, A. Quaiser, L. Bonch-Osmolovskaya, and C. Schleper. 2003. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ. Microbiol. 5:787-797.
    • (2003) Environ. Microbiol. , vol.5 , pp. 787-797
    • Ochsenreiter, T.1    Selezi, D.2    Quaiser, A.3    Bonch-Osmolovskaya, L.4    Schleper, C.5
  • 36
    • 0027331046 scopus 로고
    • Autotrophic and heterotrophic nitrification in acidic forest and native grassland soils
    • Pennington, P. I., and R. C. Ellis. 1993. Autotrophic and heterotrophic nitrification in acidic forest and native grassland soils. Soil Biol. Biochem. 25:1399-1408.
    • (1993) Soil Biol. Biochem. , vol.25 , pp. 1399-1408
    • Pennington, P.I.1    Ellis, R.C.2
  • 37
    • 0036803181 scopus 로고    scopus 로고
    • Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil
    • Pesaro, M., and F. Widmer. 2002. Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil. FEMS Microbiol. Ecol. 42:89-98.
    • (2002) FEMS Microbiol. Ecol. , vol.42 , pp. 89-98
    • Pesaro, M.1    Widmer, F.2
  • 38
    • 0034466757 scopus 로고    scopus 로고
    • Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: Implications for molecular diversity surveys
    • Purkhold, U., A. Pommerening-Röser, S. Juretschko, M. C. Schmid, H. P. Koops, and M. Wagner. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66:5368-5382.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 5368-5382
    • Purkhold, U.1    Pommerening-Röser, A.2    Juretschko, S.3    Schmid, M.C.4    Koops, H.P.5    Wagner, M.6
  • 39
    • 0141502465 scopus 로고    scopus 로고
    • 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: Extension of the dataset and proposal of a new lineage within the nitrosomonads
    • Purkhold, U., M. Wagner, G. Timmermann, A. Pommerening-Röser, and H. P. Koops. 2003. 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: Extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Microbiol. 53:1485-1494.
    • (2003) Int. J. Syst. Evol. Microbiol. , vol.53 , pp. 1485-1494
    • Purkhold, U.1    Wagner, M.2    Timmermann, G.3    Pommerening-Röser, A.4    Koops, H.P.5
  • 40
    • 0028165830 scopus 로고
    • Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens
    • Raskin, L., J. M. Stromley, B. E. Rittmann, and D. A. Stahl. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
    • (1994) Appl. Environ. Microbiol. , vol.60 , pp. 1232-1240
    • Raskin, L.1    Stromley, J.M.2    Rittmann, B.E.3    Stahl, D.A.4
  • 41
    • 0030814870 scopus 로고    scopus 로고
    • The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations
    • Rotthauwe, J. H., K. P. Witzel, and W. Liesack. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol 63:4704-4712.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 4704-4712
    • Rotthauwe, J.H.1    Witzel, K.P.2    Liesack, W.3
  • 44
    • 0029805297 scopus 로고    scopus 로고
    • Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria
    • Stephen, J. R., A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley. 1996. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62:4147-4154.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 4147-4154
    • Stephen, J.R.1    McCaig, A.E.2    Smith, Z.3    Prosser, J.I.4    Embley, T.M.5
  • 45
    • 0031904158 scopus 로고    scopus 로고
    • Analysis of β- Subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing
    • Stephen, J. R., G. A. Kowalchuk, M. A. V. Bruns, A. E. McCaig, C. J. Phillips, T. Martin Embley, and J. I. Prosser. 1998. Analysis of β- subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:2958-2965.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 2958-2965
    • Stephen, J.R.1    Kowalchuk, G.A.2    Bruns, M.A.V.3    McCaig, A.E.4    Phillips, C.J.5    Martin Embley, T.6    Prosser, J.I.7
  • 46
    • 0000905246 scopus 로고
    • Heterotrophic nitrification in an acid forest soil and by an acid-tolerant fungus
    • Stroo, H. F., T. M. Klein, and M. Alexander. 1986. Heterotrophic nitrification in an acid forest soil and by an acid-tolerant fungus. Appl. Environ. Microbiol. 52:1107-1111.
    • (1986) Appl. Environ. Microbiol. , vol.52 , pp. 1107-1111
    • Stroo, H.F.1    Klein, T.M.2    Alexander, M.3
  • 47
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4. 0. Mol. Biol. Evol. 24:1596-1599.
    • (2007) Mol. Biol. Evol. , Issue.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 48
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 49
    • 0026452892 scopus 로고
    • Nitrate production in nitrogen-saturated acid forest soils: Vertical distribution and characteristics
    • Tietema, A., W. De Boer, L. Riemer, and J. M. Verstraten. 1992. Nitrate production in nitrogen-saturated acid forest soils: vertical distribution and characteristics. Soil Biol. Biochem. 24:235-240.
    • (1992) Soil Biol. Biochem. , vol.24 , pp. 235-240
    • Tietema, A.1    De Boer, W.2    Riemer, L.3    Verstraten, J.M.4
  • 50
    • 28644435323 scopus 로고    scopus 로고
    • Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling
    • Treusch, A. H., S. Leininger, A. Kletzin, S. C. Schuster, H. P. Klenk, and C. Schleper. 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.
    • (2005) Environ. Microbiol. , vol.7 , pp. 1985-1995
    • Treusch, A.H.1    Leininger, S.2    Kletzin, A.3    Schuster, S.C.4    Klenk, H.P.5    Schleper, C.6
  • 51
    • 0001848883 scopus 로고
    • Acid sulfate soils and rice
    • International Rice Research Institute (ed. ), IRRI, Los Banõs, Philippines
    • van Breemen, N., and L. J. Pons. 1978. Acid sulfate soils and rice, p. 739-761. In International Rice Research Institute (ed. ), Soils and Rice. IRRI, Los Banõs, Philippines.
    • (1978) Soils and Rice. , pp. 739-761
    • Van Breemen, N.1    Pons, L.J.2
  • 52
    • 31844449131 scopus 로고
    • Acid sulphate soils land reclamation and water management
    • In Land Reclamation , Wageningen, Netherlands
    • van Breemen, N. 1980. Acid sulphate soils, p. 53-57. In Land Reclamation and Water Management. ILRI Publ. 27, Wageningen, Netherlands.
    • (1980) ILRI Pub. , vol.27 , pp. 53-57
    • Van Breemen, N.1
  • 53
    • 0029432009 scopus 로고    scopus 로고
    • Nitrite in soils: Accumulation and role in the formation of gaseous N compounds
    • Van Cleemput, O., and A. H. Samater. 1996. Nitrite in soils: Accumulation and role in the formation of gaseous N compounds. Fert. Res. 45:81-89.
    • (1996) Fert. Res. , vol.45 , pp. 81-89
    • Van Cleemput, O.1    Samater, A.H.2
  • 54
    • 0001477773 scopus 로고
    • Nitrification and autotrophic nitrifying bacteria in acid tea soils
    • Walker, N., and K. N. Wickramasinghe. 1979. Nitrification and autotrophic nitrifying bacteria in acid tea soils. Soil Biol. Biochem. 11:231-236.
    • (1979) Soil Biol. Biochem. , vol.11 , pp. 231-236
    • Walker, N.1    Wickramasinghe, K.N.2


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