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Journal of Environmental Science and Health, Part A
Toxic/Hazardous Substances and Environmental Engineering
Volume 56, 2021 - Issue 2
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Research Article

Differences in nitrification and ammonium-oxidising prokaryotes in the process of wetland restoration

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Pages 136-144 | Received 16 May 2020, Accepted 12 Nov 2020, Published online: 01 Dec 2020

References

  • Giguere, A. T.; Taylor, A. E.; Myrold, D. D.; Bottomley, P. J. Nitrification Responses of Soil Ammonia-Oxidizing Archaea and Bacteria to Ammonium Concentrations. Soil Sci. Soc. Am. J. 2015, 79, 1366–1374. DOI: 10.2136/sssaj2015.03.0107.
  • Li, M.; Cao, H.; Hong, Y.; Gu, J. D. Spatial Distribution and Abundances of Ammonia-Oxidizing Archaea (AOA) and Ammonia-Oxidizing Bacteria (AOB) in Mangrove Sediments. Appl. Microbiol. Biotechnol. 2011, 89, 1243–1254. DOI: 10.1007/s00253-010-2929-0.
  • Martens-Habbena, W.; Berube, P. M.; Urakawa, H.; Torre, J. R. D. L.; Stahl, D. A. Ammonia Oxidation Kinetics Determine Niche Separation of Nitrifying Archaea and Bacteria. Nature 2009, 461, 976–979. DOI: 10.1038/nature08465.
  • Beman, J. M.; Popp, B. N.; Francis, C. A. Molecular and Biogeochemical Evidence for Ammonia Oxidation by Marine Crenarchaeota in the Gulf of California. ISME J. 2008, 2, 429–441. DOI: 10.1038/ismej.2007.118.
  • French, E.; Kozlowski, J. A.; Mukherjee, M.; Bullerjahn, G.; Bollmann, A. Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater. Appl. Environ. Microbiol. 2012, 78, 5773–5780. DOI: 10.1128/aem.00432-12.
  • Mosier, A. C.; Francis, C. A. Relative Abundance and Diversity of Ammonia-Oxidizing Archaea and Bacteria in the San Francisco Bay Estuary. Environ. Microbiol. 2008, 10, 3002–3016. DOI: 10.1111/j.1462-2920.2008.01764.x.
  • Hayatsu, M.; Tago, K.; Saito, M. Various Players in the Nitrogen Cycle: Diversity and Functions of the Microorganisms Involved in Nitrification and Denitrification. Soil Sci. Plant Nutr. 2008, 54, 33–45. DOI: 10.1111/j.1747-0765.2007.00195.x.
  • Francis, C. A.; Beman, J. M.; Kuypers, M. M. M. New Processes and Players in the Nitrogen Cycle: The Microbial Ecology of Anaerobic and Archaeal Ammonia Oxidation. ISME J. 2007, 1, 19–27. DOI: 10.1038/ismej.2007.8.
  • Wang, S.; Wang, Y.; Feng, X.; Zhai, L.; Zhu, G. Quantitative Analyses of Ammonia-Oxidizing Archaea and Bacteria in the Sediments of Four Nitrogen-Rich Wetlands in China. Appl. Microbiol. Biotechnol. 2011, 90, 779–787. DOI: 10.1007/s00253-011-3090-0.
  • Hu, B. L.; Liu, S. A.; Shen, L. D.; Zheng, P.; Xu, X. Y.; Lou, L. P. Effect of Different Ammonia Concentrations on Community Succession of Ammonia-Oxidizing Microorganisms in a Simulated Paddy Soil Column. PLoS One 2012, 7, e44122.
  • Chen, X. P.; Zhu, Y. G.; Xia, Y.; Shen, J. P.; He, J. Z. Ammonia-Oxidizing Archaea: Important Players in Paddy Rhizosphere Soil? Environ. Microbiol. 2008, 10, 1978–1987. DOI: 10.1111/j.1462-2920.2008.01613.x.
  • Yao, H.; Gao, Y.; Nicol, G. W.; Campbell, C. D.; Prosser, J. I.; Zhang, L.; Han, W.; Singh, B. K. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils. Appl. Environ. Microbiol. 2011, 77, 4618–4625. DOI: 10.1128/AEM.00136-11.
  • Chmura, G. L.; Anisfeld, S. C.; Cahoon, D. R.; Lynch, J. C. Global Carbon Sequestration in Tidal, Saline Wetland Soils. Global Biogeochem. Cycles 2003, 17, 1111–1120. DOI: 10.1029/2002GB001917.
  • Sheoran, A. S.; Sheoran, V. Heavy Metal Removal Mechanism of Acid Mine Drainage in Wetlands: A Critical Review. Miner. Eng. 2006, 19, 105–116. DOI: 10.1016/j.mineng.2005.08.006.
  • Wang, G.; Jiang, M.; Wang, M.; Xue, Z. Natural Revegetation during Restoration of Wetlands in the Sanjiang Plain, Northeastern China. Ecol. Eng. 2019, 132, 49–55. DOI: 10.1016/j.ecoleng.2019.04.001.
  • Wang, C.; Li, J.; Wu, Y.; Song, Y.; Liu, R.; Cao, Z.; Cui, Y. Shifts of the nirS and nirK Denitrifiers in Different Land Use Types and Seasons in the Sanjiang Plain. J. Basic Microbiol. 2019, 59, 1040–1048. DOI: 10.1002/jobm.201900192.
  • Bossio, D. A.; Girvan, M. S.; Verchot, L.; Bullimore, J.; Borelli, T.; Albrecht, A.; Scow, K. M.; Ball, A. S.; Pretty, J. N.; Osborn, A. M. Soil Microbial Community Response to Land Use Change in an Agricultural Landscape of Western Kenya. Microb. Ecol. 2005, 49, 50–62. DOI: 10.1007/s00248-003-0209-6.
  • Gao, Y.; Mao, L.; Miao, C. Y.; Zhou, P.; Cao, J. J.; Zhi, Y. E.; Shi, W. J. Spatial Characteristics of Soil Enzyme Activities and Microbial Community Structure under Different Land Uses in Chongming Island, China: Geostatistical Modelling and PCR-RAPD Method. Sci. Total Environ 2010, 408, 3251–3260. DOI: 10.1016/j.scitotenv.2010.04.007.
  • Wu, H.; Guan, Q.; Ma, H.; Xue, Z.; Yang, M.; Batzer, D. P. Effects of Saline Conditions and Hydrologic Permanence on Snail Assemblages in Wetlands of Northeastern China. Ecol. Indic 2019, 96, 620–627. DOI: 10.1016/j.ecolind.2018.09.043.
  • Wu, H.; Lu, X.; Wu, D.; Song, L.; Yan, X.; Liu, J. Ant Mounds Alter Spatial and Temporal Patterns of CO2, CH4 and N2O Emissions from a Marsh Soil. Soil Biol. Biochem. 2013, 57, 884–891. DOI: 10.1016/j.soilbio.2012.10.034.
  • Zhang, J.; Ma, K.; Fu, B. Wetland Loss under the Impact of Agricultural Development in the Sanjiang Plain, NE China. Environ. Monit. Assess. 2010, 166, 139–148. DOI: 10.1007/s10661-009-0990-x.
  • Francis, C. A.; Roberts, K. J.; Beman, J. M.; Santoro, A. E.; Oakley, B. B. Ubiquity and Diversity of Ammonia-Oxidizing Archaea in Water Columns and Sediments of the Ocean. Proc. Natl. Acad. Sci. USA 2005, 102, 14683–14688. DOI: 10.1073/pnas.0506625102.
  • Rotthauwe, J. H.; Witzel, K. P.; Liesack, W. The Ammonia Monooxygenase Structural Gene amoA as a Functional Marker: Molecular Fine-Scale Analysis of Natural Ammonia-Oxidizing Populations. Appl. Environ. Microbiol. 1997, 62, 4704–4712.
  • Li, B.; Yang, Y.; Chen, J.; Wu, Z.; Liu, Y.; Xie, S. Nitrifying Activity and Ammonia-Oxidizing Microorganisms in a Constructed Wetland Treating Polluted Surface Water. Sci. Total Environ. 2018, 628, 310–318. DOI: 10.1016/j.scitotenv.2018.02.041
  • Tao, R.; Wakelin, S. A.; Liang, Y.; Chu, G. Response of Ammonia-Oxidizing Archaea and Bacteria in Calcareous Soil to Mineral and Organic Fertilizer Application and Their Relative Contribution to Nitrification. Soil Biol. Biochem. 2017, 114, 20–30. DOI: 10.1016/j.soilbio.2017.06.027.
  • Fang, Y.; Wang, F.; Jia, X.; Chen, J. Distinct Responses of Ammonia-Oxidizing Bacteria and Archaea to Green Manure Combined with Reduced Chemical Fertilizer in a Paddy Soil. J. Soils Sediments 2019, 19, 1613–1623. DOI: 10.1007/s11368-018-2154-5.
  • Wu, B.; Hou, S.; Peng, D.; Wang, Y.; Wang, C.; Xu, F.; Xu, H. Response of Soil Micro-Ecology to Different Levels of Cadmium in Alkaline Soil. Ecotox. Environ. Safe 2018, 166, 116–122. DOI: 10.1016/j.ecoenv.2018.09.076.
  • Xu, Z.; Wu, J.; Li, H.; Chen, Y.; Xu, J.; Xiong, L.; Zhang, J. Characterizing Heavy Metals in Combined Sewer Overflows and Its Influence on Microbial Diversity. Sci. Total Environ. 2018, 625, 1272–1282. DOI: 10.1016/j.scitotenv.2017.12.338.
  • Kurola, J.; Salkinoja-Salonen, M.; Aarnio, T.; Hultman, J.; Romantschuk, M. Activity, Diversity and Population Size of Ammonia-Oxidising Bacteria in Oil-Contaminated Landfarming Soil. FEMS Microbiol. Lett. 2005, 250, 33–38. DOI: 10.1016/j.femsle.2005.06.057.
  • Wang, X. Y.; Wang, C.; Bao, L. L.; Xie, S. G. Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Reservoir Sediment and Adjacent Soils. Appl. Microbiol. Biotechnol. 2014, 98, 1883–1892. DOI: 10.1007/s00253-013-5174-5.
  • Zhang, Y.; Chen, L.; Dai, T.; Tian, J.; Wen, D. The Influence of Salinity on the Abundance, Transcriptional Activity, and Diversity of AOA and AOB in an Estuarine Sediment: A Microcosm Study. Appl. Microbiol. Biotechnol. 2015, 99, 9825–9833. DOI: 10.1007/s00253-015-6804-x.
  • Di, H. J.; Cameron, K. C.; Shen, J.-P.; Winefield, C. S.; O'Callaghan, M.; Bowatte, S.; He, J.-Z. Ammonia-Oxidizing Bacteria and Archaea Grow under Contrasting Soil Nitrogen Conditions. FEMS Microbiol. Ecol. 2010, 72, 386–394. DOI: 10.1111/j.1574-6941.2010.00861.x.
  • Chen, X.; Zhang, L. M.; Shen, J. P.; Wei, W. X.; He, J. Z. Abundance and Community Structure of Ammonia-Oxidizing Archaea and Bacteria in an Acid Paddy Soil. Biol. Fertil. Soils 2011, 47, 323–331. DOI: 10.1007/s00374-011-0542-8.
  • Shen, J. P.; Zhang, L. M.; Zhu, Y. G.; Zhang, J. B.; He, J. Z. Abundance and Composition of Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea Communities of an Alkaline Sandy Loam. Environ. Microbiol. 2008, 10, 1601–1611. DOI: 10.1111/j.1462-2920.2008.01578.x.
  • Jia, Z.; Conrad, R. Bacteria Rather than Archaea Dominate Microbial Ammonia Oxidation in an Agricultural Soil. Environ. Microbiol. 2009, 11, 1658–1671. DOI: 10.1111/j.1462-2920.2009.01891.x.
  • Chu, H.; Fujii, T.; Morimoto, S.; Lin, X.; Yagi, K. Population Size and Specific Nitrification Potential of Soil Ammonia-Oxidizing Bacteria under Long-Term Fertilizer Management. Soil Biol. Biochem. 2008, 40, 1960–1963. DOI: 10.1016/j.soilbio.2008.01.006.
  • Di, H. J.; Cameron, K. C.; Shen, J. P.; Winefield, C. S.; O’Callaghan, M.; Bowatte, S.; He, J. Z. Nitrification Driven by Bacteria and Not Archaea in Nitrogen-Rich Grassland Soils. Nat. Geosci. 2009, 2, 621–624. DOI: 10.1038/ngeo613.
  • Wang, B.; Zhao, J.; Guo, Z.; Ma, J.; Xu, H.; Jia, Z. Differential Contributions of Ammonia Oxidizers and Nitrite Oxidizers to Nitrification in Four Paddy Soils. ISME J. 2015, 9, 1062–1075. DOI: 10.1038/ismej.2014.194.
  • Dai, Y.; Di, H. J.; Cameron, K. C.; He, J. Z. Effects of Nitrogen Application Rate and a Nitrification Inhibitor Dicyandiamide on Ammonia Oxidizers and N2O Emissions in a Grazed Pasture Soil. Sci. Total Environ. 2013, 465, 125–135. DOI: 10.1016/j.scitotenv.2012.08.091.
  • Wang, M.; Wang, S.; Long, X.; Zhuang, L.; Zhao, X.; Jia, Z.; Zhu, G. High Contribution of Ammonia-Oxidizing Archaea (AOA) to Ammonia Oxidation Related to a Potential Active AOA Species in Various Arable Land Soils. J. Soils Sediments 2019, 19, 1077–1087. DOI: 10.1007/s11368-018-2108-y.
  • He, J. Z.; Shen, J. P.; Zhang, L. M.; Zhu, Y. G.; Zheng, Y. M.; Xu, M. G.; Di, H. 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. 2007, 9, 2364–2374. DOI: 10.1111/j.1462-2920.2007.01358.x.
  • Beier, C.; Emmett, B. A.; Peñuelas, J.; Schmidt, I. K.; Tietema, A.; Estiarte, M.; Gundersen, P.; Llorens, L.; Riis-Nielsen, T.; Sowerby, A.; Gorissen, A. Gorissen, A. Carbon and Nitrogen Cycles in European Ecosystems Respond Differently to Global Warming. Sci. Total Environ. 2008, 407, 692–697. DOI: 10.1016/j.scitotenv.2008.10.001.
  • Di, H. J.; Cameron, K. C.; Podolyan, A.; Robinson, A. Effect of Soil Moisture Status and a Nitrification Inhibitor, Dicyandiamide, on Ammonia Oxidizer and Denitrifier Growth and Nitrous Oxide Emissions in a Grassland Soil. Soil Biol. Biochem. 2014, 73, 59–68. DOI: 10.1016/j.soilbio.2014.02.011.
  • Sahrawat, K. L. Factors Affecting Nitrification in Soils. Commun. Commun. Soil Sci. Plant Anal. 2008, 39, 1436–1446. DOI: 10.1080/00103620802004235.
  • Leininger, S.; Urich, T.; Schloter, M.; Schwark, L.; Qi, J.; Nicol, G. W.; Prosser, J. I.; Schuster, S. C.; Schleper, C. Archaea Predominate among Ammonia-Oxidizing Prokaryotes in Soils. Nature 2006, 442, 806–809. DOI: 10.1038/nature04983.
  • Lehtovirta-Morley, L. E.; Stoecker, K.; Vilcinskas, A.; Prosser, J. I.; Nicol, G. W. Cultivation of an Obligate Acidophilic Ammonia Oxidizer from a Nitrifying Acid Soil. Proc. Natl. Acad. Sci. 2011, 108, 15892–15897. DOI: 10.1073/pnas.1107196108.
  • Prosser, J. I.; Nicol, G. W. Candidatus Nitrosotalea. In Bergey’s Manual of Systematics of Archaea and Bacteria; Whitman PWB., Ed.,: WileyBlackwell: Hoboken, NJ, 2016, pp. 1–6.
  • Liu, S.; Shen, L.; Lou, L.; Tian, G.; Zheng, P.; Hu, B. Spatial Distribution and Factors Shaping the Niche Segregation of Ammonia-oxidizing Microorganisms in the Qiantang River, China. Appl. Environ. Microbiol. 2013, 79, 4065–4071. DOI: 10.1128/AEM.00543-13.
  • Ouyang, Y.; Norton, J. M.; Stark, J. M.; Reeve, J. R.; Habteselassie, M. Y. Ammonia-Oxidizing Bacteria Are More Responsive than Archaea to Nitrogen Source in an Agricultural Soil. Soil Biol. Biochem. 2016, 96, 4–15. DOI: 10.1016/j.soilbio.2016.01.012.
  • Xia, W.; Zhang, C.; Zeng, X.; Feng, Y.; Weng, J.; Lin, X.; Zhu, J.; Xiong, Z.; Xu, J.; Cai, Z.; Jia, Z. Autotrophic Growth of Nitrifying Community in an Agricultural Soil. ISME J. 2011, 5, 1226–1236. DOI: 10.1038/ismej.2011.5.
  • Jiang, J.; Song, Z.; Yang, X.; Mao, Z.; Nie, X.; Guo, H.; Peng, X. Microbial Community Analysis of Apple Rhizosphere around Bohai Gulf. Sci. Rep. 2017, 7, 8918. DOI: 10.1038/s41598-017-08398-9.
  • Chen, L. F.; He, Z. B.; Zhao, W. Z.; Liu, J. L.; Zhou, H.; Li, J.; Meng, Y. Y.; Wang, L. S; Soil Structure and Nutrient Supply Drive Changes in Soil Microbial Communities during Conversion of Virgin Desert Soil to Irrigated Cropland. Eur. J. Soil Sci. 2020, 71, 768–781. DOI: 10.1111/ejss.12901.
  • Li, H.; Weng, B. S.; Huang, F. Y.; Su, J. Q.; Yang, X. R. pH Regulates Ammonia-oxidizing Bacteria and Archaea in Paddy Soils in Southern China. Appl. Microbiol. Biotechnol. 2015, 99, 6113–6123. DOI: 10.1007/s00253-015-6488-2.
  • Nicol, G. W.; Leininger, S.; Schleper, C.; Prosser, J. I. The Influence of Soil pH on the Diversity, Abundance and Transcriptional Activity of Ammonia Oxidizing Archaea and Bacteria. Environ. Microbiol. 2008, 10, 2966–2978. DOI: 10.1111/j.1462-2920.2008.01701.x.
  • Liu, H.; Li, J.; Zhao, Y.; Xie, K.; Tang, X.; Wang, S.; Li, Z.; Liao, Y.; Xu, J.; Di, H.; Li, Y. Ammonia Oxidizers and Nitrite-Oxidizing Bacteria Respond Differently to Long-Term Manure Application in Four Paddy Soils of South of China. Sci. Total Environ. 2018, 633, 641–648. DOI: 10.1016/j.scitotenv.2018.03.108.
  • Xing, Y.; Si, Y. X.; Hong, C.; Li, Y. Multiple Factors Affect Diversity and Abundance of Ammonia-Oxidizing Microorganisms in Iron Mine Soil. Arch. Environ. Contam. Toxicol. 2015, 69, 20–31. DOI: 10.1007/s00244-015-0144-9.
  • Liu, W.; Wang, Z.; Zhang, Q.; Cheng, X.; Lu, J.; Liu, G. Sediment Denitrification and Nitrous Oxide Production in Chinese Plateau Lakes with Varying Watershed Land Uses. Biogeochemistry 2015, 123, 379–390. DOI: 10.1007/s10533-015-0072-9.
  • Zhao, S.; Wang, Q.; Zhou, J.; Yuan, D.; Zhu, G. Linking Abundance and Community of Microbial N2O-Producers and N2O-Reducers with Enzymatic N2O Production Potential in a Riparian Zone. Sci. Total Environ. 2018, 642, 1090–1099. DOI: 10.1016/j.scitotenv.2018.06.110.

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