Characterization of the genes involved in nitrogen cycling in wastewater treatment plants using DNA microarray and most probable number-PCR

Smith V H, Tilman G D, Nekola J C. Eutrophication: impacts of excess nutrient inputs on freshwater, marine, and terrestrial ecosystems. Environmental Pollution, 1999, 100(1-3): 179–196

Ahn Y H. Sustainable nitrogen elimination biotechnologies: a review. Process Biochemistry, 2006, 41(8): 1709–1721

Richardson D J, Watmough N J. Inorganic nitrogen metabolism in bacteria. Current Opinion in Chemical Biology, 1999, 3(2): 207–219

Zhu G B, Peng Y Z, Li B K, Guo J H, Yang Q, Wang S Y. Biological removal of nitrogen from wastewater. Reviews of Environmental Contamination and Toxicology, 2008, 192: 159–195

Song B, Tobias C R. Molecular and stable isotope methods to detect and measure anaerobic ammonium oxidation (anammox) in aquatic ecosystems. Methods in Enzymology, 2011, 496: 63–89

Kampschreur M J, Temmink H, Kleerebezem R, Jetten M S M, van Loosdrecht C M. Nitrous oxide emission during wastewater treatment. Water Research, 2009, 43(17): 4093–4103

Soda S, Arai T, Inoue D, Ishigaki T, Ike M, Yamada M. Statistical analysis of global warming potential, eutrophication potential, and sludge production of wastewater treatment in Japan. Journal of Sustainable Energy and Environment, 2013, 4(1): 33–40

Amann R I, Ludwing W, Schleifer K H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 1995, 59(1): 143–169

Prosser J I, Embley T M. Cultivation-based and molecular approaches to characterization of terrestrial and aquatic nitrifiers. Antonie van Leeuwenhoek, 2002, 81(1): 165–179

Smith C J, Osborn A M. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiology Ecology, 2009, 67(1): 6–20

He Z, Deng Y, Zhou J. Development of functional gene microarrays for microbial community analysis. Current Opinion in Biotechnology, 2012, 23(1): 49–55

Inoue D, Pang J, Matsuda M, Sei K, Nishida K, Ike M. Development of a whole community genome amplification-assisted DNA microarray method to detect functional genes involved in the nitrogen cycle. World Journal of Microbiology & Biotechnology, 2014, 30(11): 2907–2915

Hashimoto K, Matsuda M, Inoue D, Ike M. Bacterial community dynamics in a full-scale municipal wastewater treatment plant employing conventional activated sludge process. Journal of Bioscience and Bioengineering, 2014, 118(1): 64–71

Iwamoto T, Tani K, Nakamura K, Suzuki Y, Kitagawa M, Eguchi M, Nasu M. Monitoring impact of in situ biostimulation treatment on groundwater bacterial community by DGGE. FEMS Microbiology Ecology, 2000, 32(2): 129–141

Rotthauwe J H, de Boe W, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology, 1997, 63(12): 4704–4712

Sang N, Soda S, Sei K, Ike M. Effect of aeration on stabilization of organic solid waste and microbial population dynamics in lab-scale landfill bioreactors. Journal of Bioscience and Bioengineering, 2008, 106(5): 425–432

Francis C A, Roberts K J, Michael J, Santoro A E, Oakley B B. 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, 2005, 102 (41): 16683–14688

Wu L, Thompson D K, Li G, Hurt R A, Tiedje J M, Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology, 2001, 67(12): 5780–5790

Wu L, Liu X, Christopher W S, Zhou J. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole community genome amplification. Applied and Environmental Microbiology, 2006, 72(7): 4931–4941

Geets J, de Cooman M, Wittebolle L, Heylen K, Vanparys B, de Vos P, Verstraete W, Boon N. Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge. Applied Microbiology and Biotechnology, 2007, 75(1): 211–221

Wang Z, Zhang X X, Lu X, Liu B, Li Y, Long C, Li A. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing. PLoS ONE, 2014, 9(11): e113603

Shu D, He Y, Yue H, Wang Q. Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing. Bioresource Technology, 2015, 186: 163–172

Daims H, Wagner M. The microbiology of nitrogen removal. In: Seviour RJ, Nielsen PH, eds. Microbial Ecology of Activated Sludge. London: IWA Publishing, 2010,259–280

Kayee P, Sonthiphand P, Rongsayamanont C, Limpiyakorn T. Archaeal amoA genes outnumber bacterial amoA genes in municipal wastewater treatment plants in Bangkok. Microbial Ecology, 2011, 62(4): 776–788

Limpiyakorn T, Sonthiphand P, Rongsayamanont C, Polprasert C. Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants. Bioresource Technology, 2011, 102(4): 3694–3701

Wu Y J, Whang L M, Fukushima T, Chang S H. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant. Journal of Bioscience and Bioengineering, 2013, 115(4): 424–432

Burgin A J, Hamilton S K. Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Frontiers in Ecology and the Environment, 2007, 5(2): 89–96

Kraft B, Strous M, Tegetmeyer H E. Microbial nitrate respiration— genes, enzymes and environmental distribution. Journal of Biotechnology, 2011, 155(1): 104–117

Rütting T, Boeckx P, Müller C, Klemedtsson L. Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle. Biogeosciences, 2011, 8(7): 1779–1791

van den Berg E M, van Dongen U, Abbas B, van Loosdrecht M C M. Enrichment of DNRA bacteria in a continuous culture. ISME Journal, 2015, 9(10): 2153–2161

Strous M, van Gerven E, Kuenen J G, Jetten M. Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing (anammox) sludge. Applied and Environmental Microbiology, 1997, 63(6): 2446–2448

Matsuda M, Inoue D, Anami Y, Tsutsui H, Sei K, Soda S, Ike M. Comparative analysis of DNA-based microbial community composition and substrate utilisation patterns of activated sludge microorganisms from wastewater treatment plants operated under different conditions. Water Science and Technology, 2010, 61(11): 2843–2851

Takada K, Hashimoto K, Soda S, Ike M, Yamashita K, Hashimoto T. Characterization of microbial community in membrane bioreactors treating domestic wastewater. Journal of Water and Environment Technology, 2014, 12(2): 99–107

Ma Q, Qu Y, Shen W, Zhang Z, Wang J, Liu Z, Li D, Li H, Zhou J. Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing. Bioresource Technology, 2015, 179: 436–443