Allison S M, Prosser J I. 1991. Survival of ammonia oxidizing bacteria in air-dried soil. FEMS Microbiology Letters, 79, 65-68 Allison S M, Prosser J I. 1993. Ammonia oxidation at low pH by attached populations of nitrifying bacteria. Soil Biology and Biochemistry, 25, 935-941 Avrahami S, Conrad R. 2005. Cold-temperature climate: a factor for selection of ammonia oxidizers in upland soil? Canadian Journal of Microbiology, 51, 709-714 Bäckman J S K, Hermansson A, Tebbe C C. 2003. Liming induces growth of a diverse flora of ammonia-oxidizing bacteria in acid spruce forest soil as determined by SSCP and DGGE. Soil Biology and Biochemistry, 35, 1337- 1347. Bäckman J S K, Klemedtsson A K, Klemedtsson L, Lindgren P. 2004. Clear-cutting affects the ammonia- oxidizing community differently in limed and non-limed coniferous forest soils. Biology and Fertility of Soils, 40, 260-267 de Boer W, Kowalchuk G A. 2001. Nitrification on acid soils: micro-organisms and mechanisms. Soil Biology and Biochemisty, 33, 853-866 de Boer W, Laanbroek H J. 1989. Ureolytic nitrification at low pH by Nitrosospira spec. Archives of Microbiology, 152, 178-181 Boyle-Yarwood S A, Bottomley P J, Myrold D D. 2008. Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environmental Microbiology, 10, 2956-2965 Cebron A, Coci M, Garnier J, Laanbroek H J. 2004. Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: Impact of Paris wastewater effluents. Applied Environmental Microbiology, 70, 6726-6737 Chanasyk D S, Whitson I R, Mapfumo E, Burke J M, Prepas E E. 2003. The impacts of forest harvest and wildfire on soils and hydrology in temperate forests: A baseline to develop hypotheses for the Boreal Plain. Journal of Environmental Engineering and Science, 2, 51-62 Di H J, Cameron K C, Shen J P, Winefield C S, Callaghan M, Bowatte S, He J Z. 2009. Nitrification driven by bacteria and not archaea in nitrogen-rich grass-land soils. National Geoscience, 2, 621-624 F i e r e r N, Jackson R B. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 103, 626-631 Frijlink M J, Abee T, Laanbroek H J, de Boer W, Konings W N. 1992. The bioenergetics of ammonia and hydroxylamine oxidation in Nitrosomonas europaea at acid and alkaline pH. Archives of Microbiology, 157, 194-199 Freitag T E, Chang L, Prosser J I. 2006. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater marine gradient. Environmental Microbiology, 8, 684- 696. Grigal D F. 2000. Effects of extensive forest management on soil productivity. Forest Ecology and Management, 138, 167-185 Hart S C, Stark J M, Davidson E A, Firestone M K. 1994. Soil Science Society of America Book Series #5. Madison, WI. pp. 985-1018 Hastings R C, Ceccherini M T, Miclaus N, Saunders J R, Bazzicalupo M, McCarthy A J. 1997. Direct molecular biological analysis of ammonia oxidizing bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiology Ecology, 23, 45-54 He J Z, Hu H W, Zhang L M. 2012. Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biology and Biochemistry, 55, 146-154 Helgason B L Walley F L, Gemida J J. 2009. Fungal and bacterial abundance in long-term no-till and intensive- till soils of the northern Great Plains. Soil Biology and Biochemistry, 73, 120-127 Hermansson A, Backman J S K, Svensson B H. 2004, Quantification of ammonia-oxidizing bacteria in limed and non-limed acidic coniferous forest soil using real- time PCR. Soil Biology and Biochemistry, 34, 1935- 1941. Holly M H, James J, Germida. 2012. Relationship between ammonia oxidizing bacteria and bioavailable nitrogen in harvested forest soils of central Alberta. Soil Biology and Biochemistry, 46, 18-25 Jiang Q Q, Bakken L R. 1999. Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiology Ecology, 30, 171-186 Kemmitt S J, Wright D, Goulding K W T, Jones D L. 2006. pH regulation of carbon and nitrogen dynamics in two agricultural soils. Soil Biology and Biochemistry, 38, 898-911 Killham K. 1990. Nitrification in coniferous forest soils. Plant and Soil, 128, 31-44 Kong A Y Y, Hristova K, Scow K M, Six J. 2010. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments. Soil Biology and Biochemistry, 42, 1523-1533 Koops H P, Pommerening-Röser A. 2001. Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiology Ecology, 37, 1-9 Kowalchuk G A, Stephen J R. 2001. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annual Review of Microbiology, 55, 485-529 Kowalchuk G A, Stephen J R, de Boer W, Prosser J I, Embley T M, Woldendorp J W. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Applied and Environmental Microbiology, 63, 1489- 1497. Li H, Qiu J J, Wang L G, Xu M Y, Liu Z Q, Wang W. 2012. Estimates of N2O emissions and mitigation potential from a spring maize field based on DNDC model. Journal of Integrative Agriculture, 11, 2067-2078 Li Y L, Wang L, Zhang W Q, Wang H L, Fu X H, Le Y Q. The variability of soil microbial community composition of different types of tidal wetland in Chongming Dongtan and its effect on soil microbial respiration. Ecological Engineering, 37, 1276-1282 Li Z D, Wang Y H, Li L Y. 2009. Orchard soil acidification status in Jiaodong peninsula of Shandong Province and control techniques. Phosphate and Compound Fertilizer, 24, 80-81 (in Chinese) Lueders T, Friedrich M W. 2003. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Applied Environmental Microbiology, 69, 320-326 Mathieu-Daude F, Welsh J, Vogt T, McClelland M. 1996. DNA rehybridization during PCR: the ‘Cot effect’ and its consequences. Nucleic Acids Research, 24, 2080- 2086. Mahmood S, Freitag T E, Prosser J I. 2006. Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples. FEMS Microbiology Ecology, 56, 482-493 Malchair S, de Boeck H J, Lemmens C M H M, Merckx R, Nijs I, Ceulemans R, Carnol M. 2010. Do climate warming and plant species richness affect potential nitrification, basal respiration and ammonia-oxidizing bacteria in experimental grasslands? Soil Biology and Biochemistry, 42, 1944-1951 Meng H Q, Xu M G, Lü J L, He X H Li J W, Shi X J, Peng C, Wang B R, Zhang H M. 2013. Soil pH dynamics and nitrogen transformations under long-term chemical fertilization in four typical Chinese croplands. Journal of Integrative Agriculture, 12, 2092-2102. Miao Y X, Bobby A S, Zhang F S. 2011. Long-term experiments for sustainable nutrient management in China. A Review. Agronomy for Sustainable Development, 31, 397-414 Mintie A T, Heichen R S, Cromack K, Myrold D D, Bottomley P J. 2003. Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon cascade mountains. Applied and Environmental Microbiology, 69, 3129-3136 Muyzer G, de Waal E C, Uitterlinden A G. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695-700 Nicol G W, Leininger S, Schleper C, Prosser J I. 2008. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology, 10, 2966- 2978. Nicolaisen M H, Ramsing N B. 2002. Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. Journal of Microbiological Methods, 50, 189-203 Nugroho R A, Röling W F M, Laverman A M, Zoomer H R, Verhoef H A. 2005. Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils. FEMS Microbiology Ecology, 53, 473-481 Prosser J I. 1989. Autotrophic nitrification in bacteria. Advances in Microbial Physiology, 30, 125-181 Rennenberg H, Dannenmann M, Gessler A, Kreuzwiesser J, Simon J, Papen H. 2009. Nitrogen balance in forest soils: nutritional limitation of plants under climate change stresses. Plant Biology, 11, 4-23 Rowe R, Todd R, Waide J. 1977. Microtechnique for most- probable-number analysis. Applied and Environmental Microbiology, 33, 675-680 Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops H P, Wagner M. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Applied Environmental Microbiology, 66, 5368-5382 dos Santos A C F, Marques E L S, Gross E, Souza S S, Dias J C T, Brendel M, Rezende R P. 2012. Detection by denaturing gradient gel electrophoresis of ammonia- oxidizing bacteria in microcosms of crude oil- contaminated mangrove sediments. Genetics and Molecular Research, 11, 190-201 Shen J P, Zhang L M, Di H J, He J Z. 2012. A review of ammonia-oxidizing bacteria and archaea in Chinese soils. Frontiers in Microbiology, 3, 1-7 Shen X Y, Zhang L M, Shen J P, Li L H, Yuan C L, He J Z. 2011. Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semi-arid temperate grassland. Journal of Soil Sediment, 11, 1243-1252 Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599 Tong D, Xu R. 2012. Effects of urea and (NH4)2SO4 on nitrification and acidification of Ultisols from southern China. Journal of Environmental Science (in China), 24, 682-689 Wrage N, Velthof G L, van Beusichem M L, Oenema O. 2001. Role of nitrifier denitrification in the production of nitrous oxide. Soil Biology and Biochemistry, 33, 1723- 1732. Xia W W, Zhang C X, Zeng X W, Feng Y Z, Weng J H, Lin X G, Zhu J G, Xiong Z Q, Xu J, Cai Z C, et al. 2011. Autotrophic growth of nitrifying community in an agricultural soil. The ISME Journal, 5, 1226-1236 Xiao L, Liu G B, Xue S, Zhang C. 2013. Soil microbial community composition during natural recovery in the Loess Plateau, China. Journal of Integrative Agriculture, 12, 1872-1883 Yeager C M, Northup D E, Grow C C, Barns S M, Kuske C R. 2005. Changes in nitrogen-fixing and ammonia- oxidizing bacterial communities in soil of a mixed conifer forest after wildfire. Applied and Environmental Microbiology, 71, 2713-2722 |