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Articles

Variations of Abundance and Community Structure of Ammonia Oxidizers and Nitrification Activity in Two Paddy Soils Polluted by Heavy Metals

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Pages 1-10 | Received 26 Oct 2017, Accepted 26 Apr 2018, Published online: 24 Dec 2018

References

  • Arao T, Ae N. 2003. Genotypic variations in cadmium levels of rice grain. Soil Sci Plant Nutr. 49:473–9. doi:10.1080/00380768.2003.10410035.
  • Balabane M, Faivre D, Van Oort F, Dahmani-Muller H. 1999. Mutual effects of soil organic matter dynamics and heavy metals fate in a metallophyte grassland. Environ Pollut. 105:45–54. doi:10.1016/S0269-7491(98)00209-7.
  • Broos K, Mertens J, Smolders E. 2005. Toxicity of heavy metals in soil assessed with various soil microbial and plant growth assays: As comparative study. Environ Toxicol Chem. 24:634–40. doi:10.1897/04-036R.1. PMID:15779764.
  • Cavagnaro T, Jackson L, Scow K, Hristova K. 2007. Effects of arbuscular mycorrhizas on ammonia oxidizing bacteria in an organic farm soil. Microb Ecol. 54:618–26. doi:10.1007/s00248-007-9212-7. PMID:17955326.
  • Cavagnaro TR, Jackson LE, Hristova K, Scow KM. 2008. Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil. Appl Soil Ecol. 40:13–18. doi:10.1016/j.apsoil.2008.02.006.
  • Chen X, Zhang LM, Shen JP, Xu ZH, He JZ. 2010. Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils. J Soil Sediment. 10:1510–6. doi:10.1007/s11368-010-0256-9.
  • Díaz-Raviña M, Bååth E, Frostegård Å. 1994. Multiple heavy metal tolerance of soil bacterial communities and its measurement by a thymidine incorporation technique. Appl Environ Microbiol. 60:2238–47. PMID:16349314.
  • de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl DA. 2018. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol. 10:810–818.
  • Fait G, Broos K, Zrna S, Lombi E, Hamon R. 2006. Tolerance of nitrifying bacteria to copper and nickel. Environ Toxicol Chem. 25:2000–5. doi:10.1897/05-517R.1. PMID:16916017.
  • Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. 2005. Ubiquity and diversity of ammoniaoxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci. 102:14683–8. doi:10.1073/pnas.0506625102. PMID:16186488.
  • Frey B, Pesaro M, Rudt A, Widmer F. 2008. Resilience of the rhizosphere pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar. Environ Microbiol. 10:1433–49. doi:10.1111/j.1462-2920.2007.01556.x. PMID:18279346.
  • Gillan DC, Danis B, Pernet P, Joly G, Dubois P. 2005. Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment. Appl Environ Microbiol. 71:679–90. doi:10.1128/AEM.71.2.679-690.2005. PMID:15691917.
  • Giller KE, Witter E, McGrath SP. 1998. Toxicity of heavy metals to micro-organisms and microbial processes in agricultural soils: a review. Soil Biol Biochem. 30:1389–414. doi:10.1016/S0038-0717(97)00270-8.
  • Gruber N, Galloway JN. 2008. An Earth-system perspective of the global nitrogen cycle. Nature. 451:293–6. doi:10.1038/nature06592. PMID:18202647.
  • Hang X, Wang H, Zhou J, Ma C, Du C. 2009. Risk assessment of potentially toxic element pollution in soils and rice (Oryza sativa) in a typical area of the Yangtze River Delta. Environ Pollut. 157:2542–9. doi:10.1016/j.envpol.2009.03.002. PMID:19344985.
  • He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM. 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. 9:2364–74. doi:10.1111/j.1462-2920.2007.01358.x. PMID:17686032.
  • Hussain Q, Liu Y, Jin Z, Zhang A, Pan G, Li L. 2011. Temporal dynamics of ammonia oxidizer (amoA) and denitrifier (nirK) communities in the rhizosphere of a rice ecosystem from Tai Lake region. China. Appl Soil Ecol. 48:210–8. doi:10.1016/j.apsoil.2011.03.004.
  • Jia ZJ, Conrad R. 2009. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol. 11:1658–71. doi:10.1111/j.1462-2920.2009.01891.x. PMID:19236445.
  • Kemmitt SJ, Wright D, Goulding K, Jones D. 2006. pH regulation of carbon and nitrogen dynamics in two agricultural soils. Soil Biol Biochem. 38:898–911. doi:10.1016/j.soilbio.2005.08.006.
  • Konneke M, Bernhard AE, de la Torre JR, Walker C, Waterbury JB. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 437:543–6. doi:10.1038/nature03911. PMID:16177789.
  • Koops HP, Purkhold U, Pommerening-Röser A, Timmermann G, Wagner M. 2003. The lithoautotrophic ammonia-oxidizing bacteria. In: The Prokaryotes: An evolv Electron resource for the microbiological community. 3rd ed. release, 3.13. New York, USA: Springer-Verlag.
  • Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury B. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 437:543–6. doi:10.1038/nature03911. PMID:16177789.
  • Leininger S, Urich T, Schloter M, Schwark L, Qi J. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature. 442:806–9. doi:10.1038/nature04983. PMID:16915287.
  • Li X, Zhu Y, Cavagnaro T, Chen M, Sun J. 2009. Do ammonia-oxidizing archaea respond to soil Cu contamination similarly as ammonia-oxidizing bacteria?. Plant Soil. 324:209–17. doi:10.1007/s11104-009-9947-7.
  • Liu J, Zhu Q, Zhang Z, Xu J, Yang J. 2005. Variations in cadmium accumulation among rice cultivars and types and the selection of cultivars for reducing cadmium in the diet. J Sci Food Agric. 85:147–53. doi:10.1002/jsfa.1973.
  • Liu YR, Zheng YM, Shen J, Zhang LM, He JZ. 2010. Effects of mercury on the activity and community composition of soil ammonia oxidizers. Environ. Sci Pollut Res. 17:1237–44. doi:10.1007/s11356-010-0302-6.
  • Liu Y, Liu YZ, Ding Y, Zheng J, Zhou T. 2014. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from south china. PloS One. 9:e102000. doi:10.1371/journal.pone.0102000. PMID:25058658.
  • Lu R. 2000. Methods of soil and agrochemical aanalysis. Beijing (in Chinese): China Agricultural Science and Technology Press.
  • Ma J, Pan G, Wan H, Xia Y, Luo W. 2004. Investigation on heavy metal pollution in a typical area of the Pearl River Delta. Chin J Soil Sci. 35:636–8. (in Chinese)
  • McTavish H, Fuchs JA, Hooper AB. 1993. Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. J Bacteriol. 175:2436–44. doi:10.1128/jb.175.8.2436-2444.1993. PMID:8468301.
  • Mertens J, Springael D, De Troyer I, Cheyns K, Wattiau P. 2006. Long-term exposure to elevated zinc concentrations induced structural changes and zinc tolerance of the nitrifying community in soil. Environ Microbiol. 8:2170–8. doi:10.1111/j.1462-2920.2006.01100.x. PMID:17107558.
  • Mertens J, Wakelin AS, Broos K, Mclaughlin JM, Smolders E. 2010. Extent of copper tolerance and consequences for functional stability of the ammonia-oxidizing community in long-term copper contaminated soils. Environ Toxicol Chem. 29:27–37. doi:10.1002/etc.16. PMID:20821416.
  • Mertens J, Broos K, Wakelin AS, Kowalchuk AG, Springael D. 2009. Bacteria, not archaea, restore nitrification in a zinc-contaminated soil. The ISME J. 3:916–23. doi:10.1038/ismej.2009.39. PMID:19387487.
  • Muyzer G, Brinkhoff T, Nuebel U, Santegoeds C, Schafer H. 1997. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Molecular Microbial Ecology Manual. Dordrecht, The Netherlands: Kluwer Academic Publishers. p. 1–27.
  • 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. 10:2966–78. doi:10.1111/j.1462-2920.2008.01701.x. PMID:18707610.
  • Nies DH. 1999. Microbial heavy-metal resistance. Appl Microbiol Biotechnol. 51:730–50. doi:10.1007/s002530051457. PMID:10422221.
  • Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF. 2004. Application of real-time PCR to study effects of ammonium population size of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol. 70:1008–16. doi:10.1128/AEM.70.2.1008-1016.2004. PMID:14766583.
  • Oorts K, Ghesquiere U, Swinnen K, Smolders E. 2006. Soil properties affecting the toxicity of CuCl2 and NiCl2 for soil. Environ Toxicol Chem. 25:836–44. doi:10.1897/04-672R.1. PMID:16566169.
  • Prasad MNV. 2001. Metals in the environment: analysis by biodiversity. New York: CRC Press.
  • Prosser JI, Embley TM. 2002. Cultivation-based and molecular approaches to characterization of terrestrial and aquatic nitrifiers. Antonie van Leeuwenhoek. 81:165–79. doi:10.1023/A:1020598114104. PMID:12448715.
  • Renella G, Chaudri AM, Brookes PC. 2002. Fresh additions of heavy metals do not model long-term effects on microbial biomass and activity. Soil Biol Biochem. 34:121–4. doi:10.1016/S0038-0717(01)00150-X.
  • Rousk J, Brookes PC, Bååth E. 2009. Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization. Appl Environ Microbiol. 75:1589–96. doi:10.1128/AEM.02775-08. PMID:19151179.
  • Ruyters S, Mertens J, Springael D, Smolders E. 2010. Stimulated activity of the soil nitrifying community accelerates community adaptation to Zn stress. Soil Biol Biochem. 42:766–72. doi:10.1016/j.soilbio.2010.01.012.
  • Schleper C, Jurgens G, Jonuscheit M. 2005. Genomic studies of uncultivated archaea. Nat Rev Microbiol. 3:479–88. doi:10.1038/nrmicro1159. PMID:15931166.
  • Schmidt EL, Belser LW. 1994. Autotrophic nitrifying bacteria. In: Methods of soil analysis. Part 2. Microbiological and biochemical properties. Madison, Wis.: Soil Science Society of America, pp 159–77.
  • Smolders E, Brans K, Coppens F, Merckx R. 2001. Potential nitrification rate as a tool for screening toxicity in metal contaminated soils. Environ Toxicol Chem. 20:2469–74. doi:10.1002/etc.5620201111. PMID:11699771.
  • Smolders E, Buekers J, Oliver I, McLaughlin M. 2004. Soil properties affecting toxicity of zinc to soil microbial properties in laboratory-spiked and field-contaminated soils. Environ Toxicol Chem. 23:2633–40. doi:10.1897/04-27. PMID:15559278.
  • Stephen J, Chan Y, Macnaughton S, Kowalchuk G, Leung K. 1999. Effect of toxic metals on indigenous soil β-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Appl Environ Microbiol. 65:95–101. PMID:9872765.
  • van Beelen P, Wouterse M, Posthuma L, Rutgers M. 2004. Location-specific ecotoxicological risk assessment of metal-polluted soils. Environ Toxicol Chem. 23:2769–79. doi:10.1897/03-568. PMID:15559294.
  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 304:66–74. doi:10.1126/science.1093857. PMID:15001713.
  • Wu X, Pan G, Li L. 2006. Study on soil quality change in the Yangtze River Delta. Geography Geo-Information Sci. 22:88–91. (in Chinese)
  • Wu Y, Chen T, Kong Q. 1986. Heavy metals pollution and control of agricultural soils in China. Chin J Soil Sci. 4:187–9. (in Chinese)
  • Xia Y, Zhu Y, Gu Q, He J. 2007. Does long-term fertilization treatment affect the response of soil ammonia-oxidizing bacterial communities to Zn contamination?. Plant Soil. 301:245–54. doi:10.1007/s11104-007-9441-z.
  • Xu C, Xia B, Qin J, He S, Li H. 2007. Analysis and evaluation on heavy metal contamination in paddy soils in the lower stream of Dabaoshan Area, Guangdong Province. J Agro-Environ Sci. 26:549–53. (in Chinese)

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