pH regulates key players of nitrification in paddy soils
Tóm tắt
Từ khóa
Tài liệu tham khảo
Allison, 1993, Ammonia oxidation at low pH by attached populations of nitrifying bacteria, Soil Biology and Biochemistry, 25, 935, 10.1016/0038-0717(93)90096-T
Alves, 2013, Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea, The ISME Journal, 7, 1620, 10.1038/ismej.2013.35
Avrahami, 2003, Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures, Applied and Environmental Microbiology, 69, 6152, 10.1128/AEM.69.10.6152-6164.2003
Avrahami, 2002, Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers, Applied and Environmental Microbiology, 68, 5685, 10.1128/AEM.68.11.5685-5692.2002
Bedard-Haughn, 2006, Land use effects on gross nitrogen mineralization, nitrification, and N2O emissions in ephemeral wetlands, Soil Biology and Biochemistry, 38, 3398, 10.1016/j.soilbio.2006.05.010
Burton, 2001, Autotrophic ammonia oxidation at low pH through urea hydrolysis, Applied and Environmental Microbiology, 67, 2952, 10.1128/AEM.67.7.2952-2957.2001
Chen, 2011, Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil, Biology and Fertility of Soils, 47, 323, 10.1007/s00374-011-0542-8
Curtin, 1998, Effects of acidity on mineralization: pH-dependence of organic matter mineralization in weakly acidic soils, Soil Biology and Biochemistry, 30, 57, 10.1016/S0038-0717(97)00094-1
Deboer, 1992, The chemolithotrophic ammonium-oxidizing community in a nitrogen-saturated acid forest soil in relation to pH-dependent nitrifying activity, Soil Biology and Biochemistry, 24, 229, 10.1016/0038-0717(92)90223-K
Di, 2009, Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils, Nature Geoscience, 2, 621, 10.1038/ngeo613
Erguder, 2009, Environmental factors shaping the ecological niches of ammonia-oxidizing archaea, FEMS Microbiology Reviews, 33, 855, 10.1111/j.1574-6976.2009.00179.x
FAO (Food and Agriculture Organization), U, 1988, 212
FAOSTAT, 2010
Francis, 2005, Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean, Proceedings of the National Academy of Sciences of the United States of America, 102, 14683, 10.1073/pnas.0506625102
Hatzenpichler, 2012, Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea, Applied and Environmental Microbiology, 78, 7501, 10.1128/AEM.01960-12
He, 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, Environmental Microbiology, 9, 2364, 10.1111/j.1462-2920.2007.01358.x
Jia, 2009, Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil, Environmental Microbiology, 11, 1658, 10.1111/j.1462-2920.2009.01891.x
Könneke, 2005, Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, 437, 543, 10.1038/nature03911
Könneke, 2014, Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation, Proceedings of the National Academy of Sciences of the United States of America, 111, 8239, 10.1073/pnas.1402028111
Ke, 2013, Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil, Environmental Microbiology, 15, 2275, 10.1111/1462-2920.12098
Kemmitt, 2006, pH regulation of carbon and nitrogen dynamics in two agricultural soils, Soil Biology and Biochemistry, 38, 898, 10.1016/j.soilbio.2005.08.006
Kikuchi, 2007, Molecular analyses reveal stability of bacterial communities in bulk soil of a Japanese paddy field: estimation by denaturing gradient gel electrophoresis of 16S rRNA genes amplified from DNA accompanied with RNA, Soil Science and Plant Nutrition, 53, 448, 10.1111/j.1747-0765.2007.00177.x
Killham, 1990, Nitrification in coniferous forest soils, Plant and soil, 128, 31, 10.1007/BF00009394
Kim, 2012, Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I. 1b from an agricultural soil, Environmental Microbiology, 14, 1528, 10.1111/j.1462-2920.2012.02740.x
Kirk, 2004, Methods of studying soil microbial diversity, Journal of Microbiological Methods, 58, 169, 10.1016/j.mimet.2004.04.006
Kowalchuk, 1998, Community analysis of ammonia-oxidising bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation, FEMS Microbiology Ecology, 27, 339, 10.1111/j.1574-6941.1998.tb00550.x
Kowalchuk, 2001, Ammonia-oxidizing bacteria: a model for molecular microbial ecology, Annual Review of Microbiology, 55, 485, 10.1146/annurev.micro.55.1.485
Lam, 2007, Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea, Proceedings of the National Academy of Sciences of the United States of America, 104, 7104, 10.1073/pnas.0611081104
Lan, 2014, Temperature dependence of gross N transformation rates in two Chinese paddy soils under aerobic condition, Biology and Fertility of Soils, 1
Lehtovirta-Morley, 2011, Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil, Proceedings of the National Academy of Sciences of the United States of America, 108, 15892, 10.1073/pnas.1107196108
Lehtovirta, 2009, Soil pH regulates the abundance and diversity of Group 1.1 c Crenarchaeota, FEMS Microbiology Ecology, 70, 367, 10.1111/j.1574-6941.2009.00748.x
Leininger, 2006, Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature, 442, 806, 10.1038/nature04983
Li, 2014, Application of membrane inlet mass spectrometry to directly quantify denitrification in flooded rice paddy soil, Biology and Fertility of Soils, 1
Lu, 2013, Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils, Environmental Microbiology, 15, 1795, 10.1111/1462-2920.12071
Martens-Habbena, 2009, Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria, Nature, 461, 976, 10.1038/nature08465
Nicol, 2008, The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria, Environmental Microbiology, 10, 2966, 10.1111/j.1462-2920.2008.01701.x
Nicolaisen, 2004, Nitrification–denitrification dynamics and community structure of ammonia oxidizing bacteria in a high yield irrigated Philippine rice field, FEMS Microbiology Ecology, 49, 359, 10.1016/j.femsec.2004.04.015
Nishimura, 2004, Methane and nitrous oxide emissions from a paddy field with Japanese conventional water management and fertilizer application, Global Biogeochemical Cycles, 18, 10.1029/2003GB002207
Nishio, 1994, Effects of organic acids on heterotrophic nitrification by Alcaligenes faecalis OKK17, Bioscience, Biotechnology, and Biochemistry, 58, 1574, 10.1271/bbb.58.1574
Nugroho, 2007, Low nitrification rates in acid Scots pine forest soils are due to pH-related factors, Microbial Ecology, 53, 89, 10.1007/s00248-006-9142-9
Nugroho, 2009, Changes in nitrification and bacterial community structure upon cross-inoculation of Scots pine forest soils with different initial nitrification rates, Soil Biology and Biochemistry, 41, 243, 10.1016/j.soilbio.2008.10.020
Offre, 2009, Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene, FEMS Microbiology Ecology, 70, 99, 10.1111/j.1574-6941.2009.00725.x
Paul, 1989
Prosser, 2002, Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers, Antonie van Leeuwenhoek, 81, 165, 10.1023/A:1020598114104
Prosser, 2012, Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation, Trends in Microbiology, 20, 523, 10.1016/j.tim.2012.08.001
Radajewski, 2000, Stable-isotope probing as a tool in microbial ecology, Nature, 403, 646, 10.1038/35001054
Rotthauwe, 1997, The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations, Applied and Environmental Microbiology, 63, 4704, 10.1128/AEM.63.12.4704-4712.1997
Schimel, 1984, Identification of heterotrophic nitrification in a Sierran forest soil, Applied and Environmental Microbiology, 48, 802, 10.1128/AEM.48.4.802-806.1984
Shen, 2008, Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam, Environmental Microbiology, 10, 1601, 10.1111/j.1462-2920.2008.01578.x
Stahl, 2012, Physiology and diversity of ammonia-oxidizing archaea, Annual Review of Microbiology, 66, 83, 10.1146/annurev-micro-092611-150128
Stephen, 1998, Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing, Applied and Environmental Microbiology, 64, 2958, 10.1128/AEM.64.8.2958-2965.1998
Stephen, 1996, Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria, Applied and Environmental Microbiology, 62, 4147, 10.1128/AEM.62.11.4147-4154.1996
Strayer, 1981, Effect of simulated acid rain on nitrification and nitrogen mineralization in forest soils, Journal of Environmental Quality, 10, 547, 10.2134/jeq1981.00472425001000040026x
Suzuki, 1974, Ammonia or ammonium ion as substrate for oxidation by Nitrosomonas europaea cells and extracts, Journal of Bacteriology, 120, 556, 10.1128/JB.120.1.556-558.1974
Tourna, 2008, Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms, Environmental Microbiology, 10, 1357, 10.1111/j.1462-2920.2007.01563.x
Tourna, 2011, Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil, Proceedings of the National Academy of Sciences of the United States of America, 108, 8420, 10.1073/pnas.1013488108
Wang, 2014, Active ammonia oxidizers in an acidic soil are phylogenetically closely related to neutrophilic archaeon, Applied and Environmental Microbiology, 80, 1684, 10.1128/AEM.03633-13
Wessén, 2010, Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management, Soil Biology and Biochemistry, 42, 1759, 10.1016/j.soilbio.2010.06.013
Whitby, 2001, 13C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations, Letters in Applied Microbiology, 32, 398, 10.1046/j.1472-765X.2001.00930.x
Wuchter, 2006, Archaeal nitrification in the ocean, Proceedings of the National Academy of Sciences of the United States of America, 103, 12317, 10.1073/pnas.0600756103
Xia, 2011, Autotrophic growth of nitrifying community in an agricultural soil, The ISME Journal, 5, 1226, 10.1038/ismej.2011.5