Long-term application of organic manure changes abundance and composition of ammonia-oxidizing archaea in an acidic red soil

REFERENCES

• Arp DJ, Chain PSG, Klotz MG 2007: The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu. Rev. Microbiol., 61, 503–528. doi:10.1146/annurev.micro.61.080706.093449
   PubMed Web of Science ®Google Scholar
• Chen X, Zhang LM, Shen JP, Wei WX, He JZ 2011: Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil. Biol. Fertil. Soils, 47, 323–331. doi:10.1007/s00374-011-0542-8
   Web of Science ®Google Scholar
• Chen XP, Zhu YG, Xia Y, Shen JP, Jz H 2008: Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environ. Microbiol., 10, 1978–1987.
   PubMed Web of Science ®Google Scholar
• Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB 2005: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. USA, 102, 14683–14688. doi:10.1073/pnas.0506625102
   PubMed Web of Science ®Google Scholar
• Hatzenpichler R 2012: Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl. Environ. Microbiol., 78, 7501–7510. doi:10.1128/AEM.01960-12
   PubMed Web of Science ®Google Scholar
• He JZ, Hu HW, Zhang LM 2012: Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biol. Biochem., 55, 146–154. doi:10.1016/j.soilbio.2012.06.006
   Web of Science ®Google Scholar
• He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di HJ 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. doi:10.1111/j.1462-2920.2007.01358.x
   PubMed Web of Science ®Google Scholar
• He JZ, Zheng Y, Chen CR, He YQ, Zhang LM 2008: Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches. J. Soils Sediments, 8, 349–358. doi:10.1007/s11368-008-0025-1
   Web of Science ®Google Scholar
• Huang R, Wu YC, Zhang JB, Zhong WH, Jia ZJ, Cai ZC 2012: Nitrification activity and putative ammonia-oxidizing archaea in acidic red soils. J. Soils Sediments, 12, 420–428. doi:10.1007/s11368-011-0450-4
   Web of Science ®Google Scholar
• Kowalchuk GA, Stephen JR 2001: Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbial., 55, 485–529. doi:10.1146/annurev.micro.55.1.485
   PubMed Web of Science ®Google Scholar
• Lu RK 2000: Methods of Soil Agricultural Chemical Analysis. China Agriculture Science & Technology Press, Beijing.
   Google Scholar
• Nicol GW, Leininger S, Schleper C, Prosser JI 2008: The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ. Microbiol., 10, 2966–2978. doi:10.1111/j.1462-2920.2008.01701.x
   PubMed Web of Science ®Google Scholar
• Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ 2008: Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ. Microbiol., 10, 1601–1611. doi:10.1111/j.1462-2920.2008.01578.x
   PubMed Web of Science ®Google Scholar
• Stahl DA, De La Torre J 2012: Physiology and diversity of ammonia-oxidizing archaea. Annu. Rev. Microbiol., 66, 83–101. doi:10.1146/annurev-micro-092611-150128
   PubMed Web of Science ®Google Scholar
• Stopnisek N, Gubry-Rangin C, Höfferle S, Nicol GW, Mandic-Mulec I, Prosser JI 2010: Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. Appl. Environ. Microbiol., 76, 7626–7634. doi:10.1128/AEM.00595-10
   PubMed Web of Science ®Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S 2007: MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596–1599. doi:10.1093/molbev/msm092
   PubMed Web of Science ®Google Scholar
• Taylor AE, Zeglin LH, Dooley S, Myrold DD, Bottomley PJ 2010: Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils. Appl. Environ. Microbiol, 76, 7691–7698. doi:10.1128/AEM.01324-10
   PubMed Web of Science ®Google Scholar
• Xue D, Yao HY, Huang CY 2006: Microbial biomass, N mineralization and nitrification, enzyme activities, and microbial community diversity in tea orchard soils. Plant Soil, 288, 319–331. doi:10.1007/s11104-006-9123-2
   Web of Science ®Google Scholar
• Yao HY, Gao YM, Nicol GW, Campbell CD, Prosser JI, Zhang LM, Han WY, Singh BK 2011: Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Appl. Environ. Microbiol., 77, 4618–4625. doi:10.1128/AEM.00136-11
   PubMed Web of Science ®Google Scholar
• Zhang LM, Hu HW, Shen JP, He JZ 2012: Ammnoia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J., 6, 1032–1045. doi:10.1038/ismej.2011.168
   PubMed Web of Science ®Google Scholar
• Zhao QG 2002: Mechanism, temporal-spatial changes and controlling countermeasures of soil degradation in hilly red soil region of Southeastern China, 290–332. Science Press, Beijing.
   Google Scholar
• Zhong WH, Cai ZC 2007: Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl. Soil Ecol., 36, 84–91. doi:10.1016/j.apsoil.2006.12.001
   Web of Science ®Google Scholar
• Zhong WH, Gu T, Wang W, Zhang B, Lin XG, Huang QR, Shen WS 2010: The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil, 326, 511–522. doi:10.1007/s11104-009-9988-y
   Web of Science ®Google Scholar