本研究主要針對畜牧廢水場及都市污水處理場的好氧活性污泥，進行硝化菌生態以及硝化效能的相關研究。本研究除了以傳統研究方法對廢水處理場之廢水特性、硝化效能以及活性污泥硝化動力實驗進行深入探討外，並且以分子生物技術―尾端修飾限制酵素片段長度多形性(terminal restriction fragment length polymorphism; T-RFLP)監測好氧活性污泥中，氨氧化菌及亞硝酸氧化菌的族群分佈與動態變化。
本研究所針對之污水處理廠，包含一都市污水處理廠以及一畜牧廢水處理廠，在畜牧廢水好氧生物處理單元進流水中有215~245mg N/L的凱氏氮與0.1~0.3 mg N/L 的硝酸氮，出流水中有180~210 mg N/L 的硝酸氮與16~26mg N/L的凱氏氮，畜牧廢水處理廠整體的硝化效率在70％以上。此外，亞硝酸氮在好氧生物處理單元進流水中有0.01 mg N/L，出流水中則有5～15 mg N/L，略呈現出亞硝酸氮的累積。在都市污水好氧生物處理單元進流水中，只有17~21 mg N/L的凱氏氮與不到0.1 mg N/L 的硝酸氮，約畜牧廢水的1/10，其中以氨氮為主，在汙水廠出流水中有17~25 mg N/L 的硝酸氮與2.5~4.5mg N/L的凱氏氮，整體有60～80％的凱氏氮會因硝化作用轉換成硝酸氮，並且亞硝酸在進流與出流皆低於0.1 mg N/L，無顯著之累積情形。
本研究中所使用的T-RFLP方法包含16S rDNA與功能性基因amoA(Park et al., 2002)。在本研究中，畜牧廢水場及都市污水處理場的16S rDNA為主銨氧化菌T-RFLP結果明顯皆以Nitrosomonas菌屬為主，兩處理廠皆未偵測到明顯之Nitrosospira存在。在亞硝酸氧化菌方面，Nitrospira與Nitrobacter這兩屬菌同時為長期存在於畜牧與都市污水場的優勢亞硝酸氧化菌。
在功能性基因T-RFLP方面，處理含高氮廢水的畜牧廢水場中，Nitrosomonas europaea 為長期存在於活性污泥中的優勢氨氧化菌，此外，Nitrosospira、N. communis與N. cryotolerans這些同樣具有生長在含有高氨氮營養基質特性的氨氧化菌也在畜牧廢水場的T-RFLP結果中出現。在處理含相對低氮廢水的都市污水處理場中，Nitrosomonas oligotropha 這株具有較低氨氮半飽和常數的氨氧化菌為長期存在於活性污泥中的優勢菌。
除T-RFLP之外，本研究亦有選殖定序實驗。處理含高氮廢水的畜牧廢水場中，Nitrosomonas europaea 為長期存在於活性污泥中的優勢氨氧化菌，都巿污水廠則以Nitrosomonas oligotropha與Nitrosomonas sp. Nm143 lineage為長期存在於活性污泥中的優勢氨氧化菌族群。

This study evaluate microbial ecology and performance of nitrification of active sludge in different municipal and swine waste water treatment plant. Besides of traditional method to investigate characteristic of waste water, performance of nitrification and dynamic nitrification experiment of active sludge, this study used molecular biology techniques - terminal restriction fragment length polymorphism(T-RFLP) to investigate population transfer of ammonia oxydizing bacteria(AOB) and nitrite oxydizing bacteria (NOB).

The subjec this syudy investigate contain a municipal waste water treatment plant and a swine waste water treatment plant. Ammonium in swine waste water inflow has reached to 215~245 mg N/L, and nitrate in outflow has reached to 180~210 mg N/L. Nitrite accumulation in outflow has reached to 5~15 mg N/L with totally nitrification effency more than 70%. TKN in municipal waste water inflow is only one of ten in swine waste water inflow. Most of TKN is ammonium with 60~80% nitrification transform efficiency. No obvious nitrite accumulation in municipal waste water outflow.

T-RFLP in this study compose of 16S rDNA and fuctional gene amoA (Park et al., 2002). In 16S rDNA based T-RFLP result, Nitrosomonas is dominant AOB in municipal and swine waste water treatment without significant Nitrosospira signal. Long term dominant NOB in this two waste water treatment are Nitrobacter and Nitrospira.

In amoA based T-RFLP result, Nitrosomonas europaea is long term dominant in swine waste water treatment. Besides of Nitrosomonas europaea, amoA based T-RFLP detected signal of Nitrosospira, N. communis and N. cryotolerans which exist in high nitrogen condition in swine waste water treatment. Nitrosomonas oligotropha is long term dominant AOB in municipal waste water treatment with low nitrogen condition comparing with swine waste water treatment.

Moreover, this study used cloning-sequencing experiment to investigate AOB in municipal and swine waste water treatment. In cloning-sequencing results, Nitrosomonas europaea is dominant AOB in swine waste water treatment, and Nitrosomonas oligotropha and Nitrosomonas sp. Nm143 lineage is dominant AOB in municipal waste water treatment.

Amann, R. I., Binder, B. J., Olson, R. J., Chisholm, S. W., Devereux, R., and Stahl, D. A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56(6), 1919-1925.
Amann, R. I., Ludwig, W., and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59, 143.
Argaman, Y., Sedlak, R. I., Eckenfelder, W. W., Daigger, G. T., and Poison, S. R. (1991) Phosphorus and Nitrogen Removal from Municipal Wastewater-Principles and Practice , 2nd Ed. , Lewis Publishers.
Avaniss-Aghajani, E., Jones, K., Holtzman, A., Glover, T., Boian, M., Froman, S., and Brunk, C. F. (1996) Molecular technique for rapid identification of Mycobacteria, J Clin Microbiol. 34 98-102.
Bano, N. and Hollibaugh, J. T. (2000). Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean. Appl. Environ. Microbiol. 66, 1960–1969.
Bock, E., Koops, H. P., Harms, H., and Ahlers, B. (1991). The biochemistry of nitrifying organisms. In Variations in autotrophic life. Vol. eds J. M. Shively and L. L. Barton Academic Press Inc., San Diego, CA, 171-200.
Boer, W. D., and Kowlchuk, G. A. (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Bio. Biochem. 33:853-66.
Braker, G., Ayala-Del-Rio, H. L., Devol, A. H., Fesefeldt, A., and Tiedje, J. M. (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. Vol. 67, p. 1893-1901.
Bruce, K. D. (1997) Analysis of mer gene subclass within bacterial communities in soil and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. Vol. 63, p. 4914-4919.
Cancilla, M. R., Powell, I. B., Hillier, A. J., and Davidson, B. E. (1992) Rapid genomic fingerprinting of Lactococcus lactis strain by arbitrarily primed polymerase chain reaction with 32P and fluorescent labels, Appl. Environ. Microbiol. 58 1772–1775.
Charley, R. C., Hooper, D. G.,and McLee, A. G. (1980) Nitrification kinetics in activated sludge at various temperatures and dissolved oxygen concentrations. Wat. Res. 14 (12): 1387-1396.
Chudoba, J., Eech, J. S., Chudoba, P. (1985) The effect of aeration tank configuration on nitrification kinetics. J. WPCF. 57 (11): 1078-1083.
Clement, B. G., Kehl, L. E., DeBord, K. L., and Kitts, C. L. (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR based method for the complex bacterial communities, J. Microbiol. Methods, Vol. 31, p. 135-142 .
Dollhopf, S. L., Hashsham, S. A., and Tiedje, J. M. (2001) Interpreting 16S rDNA T-RFLP Data: Application of Self-Organizing Maps and Prrincipal Component Analysis to Describe Community Dynamics and Convergence. Microaial Ecology, Vol. 42, p. 495-505 .
Ferris, M. J., Muyzer G., and Ward D. W. (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ.Microbiol.62(2), 340-346
Focht, D. D., and Verstrate, W. (1977) Biochemical ecology of nitrification and denitrification. Adv. Microbial Ecol. 1: 135-214.
Focht, D.L., and Chang, A. C. (1975)“Nitrification and Denitrification Process Related to Wastewater Treatment.” Adv. Appl. Microbiol., 20, 153.
Freitag, T. E., and Prosser, J. I. (2003) Community structure of ammonia-oxidizing bacteria within anoxic marine sediments.Appl. Environ. Microbiol. 69, 1359–1371.
Gee, C. S., Suidan, M. T., and Pfeffer, J. T. (1990) Modeling of nitrification under substrate-inhibiting conditions, J. Environ. Engrg. ASCE 116(1): 18-31.
Grady, C. P. L., Daigger, G. T., and Lim, H. C. (1999) Biological wastewater treatment. 2nd ed. Marcel Dekker, Inc., NewYork, NY.
Grunditz, C., and Dalhammer, G. (2001) Development of nitrification inhibition assays using pure cultures of Nitrosomonas and Nitrobacter. Wat. Res. Vol. 35, No. 2, pp. 433±440.
Hastings, R. C., Ceccherini,M. T., Miclaus, N. , Saunders,J. R., Bazzicalupo, M., and McCarthy,A. J. (1997) Direct molecular biological analysis of ammonia oxidizing bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol. Ecol. 23:45–54.
Head, I. M., Saunders, J. R., and Pickup, R. W. (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35:1-21.
Hiorns, W. D., Hastings, R. C., Head, I. M., McCarthy, A. J., Saunders, J. R., Pickup, R. W., and Hall, G. H. (1995) Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of Nitrosospira in the environment. Microbiol. 141, 2793.
Hollibaugh, J. T., Bano, N., and Ducklow, H. W. (2002). Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 68, 1478–1484.
Holmes, A. J., Costello, A., Lidstorm, M. E., and Murrell, J. C. (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionary related. FEMS Microbiol. Lett. 132 pp203-208.
Holt G. J., Krieg R. N., Sneath H. P., Staley T. J., and Williams T. S. (1994)Bergey’s manual of determinative bacteriology.9th Edition, Williams and Wilkins,Maryland.
Hommes M. G., Sayavedra-soto, L. A., and Arp. D. J. (2001) Transcript analysis of multiple copies of amo (encoding ammonia monooxygenase) and hao (encoding hydroxylamine oxydoreductase) in Nitrosomonas europaea. J. Bacteriol. 183:1096-1100.
Hooper A. B., and Terry K. R. (1973)“Specific Inhibitors of Ammonia Oxidation in Nitrosomonas”, J. Bact. 115:480，
Horz, H. P., Rotthauwe, J. H., Lukow, T., and Liesack, W. (2000) Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products. J. Microbiol. Methods 39, 197.
Jonsson, K., Grunditz, C., Dalhammer, G., and Jansen, J. L. C. (2000) Occurenceof nitrification inhibition in swedish municipal wastewaters. Wat. Res. Vol. 34, No. 9, pp. 2455±2462,
Juretschko, S., Timmermann, G., Schmid, M., Schleife,r K. H., Pommerening-Roser, A., Koops, H. P., and Wagner M.(1998) Combined molecular and conventional analysis of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl. Environ . Microbiol.64 (8),3042-3051
Kane, M. D., Poulsen, L. K., and Stahl, D. A.(1993) Monitoring the enrichment and isolation of sulfate reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequence. Appl. Environ.Microbiol. 147:73-79.
Kent, A. D., Smith, D. J., Benson, B. J., Triplett, E. W. (2003) Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities, Appl. Environ. Microbiol. p. 6768-6776 .
Klotz, M. G., Alzerreca, J., and Norton, J. M. (1997) A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia oxidizing bacteria: a third member of the amo operon. FEMS. Microbiol. Lett. 150:65-73.
Knowles, G., Downing, A. L., and Barrett, M. J. (1965) Determination of kinetic constants for nitrifying bacteria in mixed culture, with the aid of an electronic computer. J. General Microbiol. 38:263-278.
Koeleman, J. G. M., Stoof, J., Biesmans, D. J., and Savelkoul, P. H. M. (1998) CMJE Vanderbroucke-Grauls, Comparison of amplified ribosomal analysis DNArestriction analysis, random amplified polymorphic DNA analysis, and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii, J Clin Microbiol. 36 2522-2529
Konstantinidis, K.T., Isaacs, N., Fett, J., Simpson, S., Long, D. T., and Marsh, T. L. (2003) Microbial diversity and resistance to copper in metal-contaminated lake sediment. Microb. Ecol., Vol. 45, p. 191-202.
Koops, H. P., and Pommerening-Roser, A. (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol. Ecol. 37, 1
Levitt, R. C., Kiser, M. B., Dragwa, C., Jedlicka, A. E., Xu, J., Meyers, D. A., and Hudson, J. R. (1994) Fluorescence-based resource for semiautomated gemonic analyses using microsatellite maker, Genomics. 24 361-365.
Lin, C., and Stahl, D. A. (1995) Taxon-specific probes for the cellulolytic genes Fibrobacter reveal abundant and novel equine-associated populations. Appl.Environ. Microbiol. 61: 1348-1351.
Liu, W. T., Marsh, T. L., Cheng, H., and Forney, L. J. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63 (11), 4516-4522.
Lueders, T., and Friedrich, M. (2000) Archaeal Population Dynamics during Sequential Reduction Processes in Rice Field Soil. Appl. Environ. Microbiol. Vol. 66, p. 2732-2742 .
Lueders, T., Chin, K. J., Conrad, R., and Friedrich, M. (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage, Environ. Microbiol. 3 194- 204.
Marsh, T. L., Liu, W. T., Forney, L. J. and Cheng, H. (1998) Beginning a molecular analysis of the eukaryal community in activated sludge, Water. Sci. Technol. 37455-460.
Marsh, T. L., Saxman, P., Cole, J., and Tiedje, J. (2000) Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis. Appl. Environ. Microbiol. p. 3616-3620 .
McCaig, A. E., Embley,T. M., and Prosser,J. I. (1994) Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol. Lett.120:363–368.
McCarthy, G. W. (1999) Modes of action of nitrification inhibitors. Biol. Fertil. Soils. 29:1-9.
McTavish, H., Fuchs, J. A., and Hooper, A. B. (1993) Sequence of the gene coding for ammonia monooxgenase in Nitrosomonas europaea. J. Bacteriol. 175:2436-2444.
Metcalf & Eddy (1991) Wastewater Engineering-treatment : disposal and reuse, 3nd, New YorK, McGraw-HILL.
Metcalf & Eddy (2003) Wastewater Engineering. McGraw Hill Companies, Inc.
Mobarry, B. K., Wagner, M., Urbain, V., Rittmann, B. E., and Stahl, D. A. (1996) Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. App. Environ. Microbiol. 62, 2156.
Moeseneder, M. M., Winter, C., Arrieta, J. M., and Herndl, G. J. (2001) Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J. Microbiol. Methods. Vol. 44, p. 159-172.
Muyzer G. and Ramsing, N. B. (1995) Molecular methods to study the organization of microbial communities. Water Sci. Technol. 32:1-9.
Okabe, S., Satoh, H., and Watanabe, Y. (1999) In situ analysis of nitrifying biofilms as determined by in situ hybridization and the use of microelectrodes. Appl. Enivon. Microbiol. 65(7):3182–91.
Olsen G. J., Lane, D. J., Giovannoni, S. J. and Pace,N. P. (1986) Microbial ecology and evolution: a ribosomal RNA approach. Ann. Rev. Microbiol. 40:337-365.
Painter, H.A. (1970) A review of literature on inorganic nitrogen metabolism in microorganisms. Wat. Res. 4: 393-450.
Park, H. D., and Noguera, R. D. (2004) Evaluating the effect of dissolved oxygen on ammonia-oxidizing bacterial communities in activated sludge. Wat. Res. 38 (2004) 3275–3286.
Park, H. D., Regan, J. M., and Noguera, D. R. (2002) Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic Orbal processes. Wat. Sci. Techno. Vol 46 No 1-2 pp 273-280
Phillips, C. J., Smith, Z., Embley, T. M., and Prosser, J. I. (1999).Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Northwestern Mediterranean Sea. Appl. Environ. Microbiol. 65, 779–786.
Poduska, R. A. (1974)“Dynamics of Nitrification in the Activated Sludge Process”, In Proceeding of the 29th Industrial Waste Conference Purdue University, West Lafayette, Ind. USA
Pommerening-Roser, A., Rath, G., and Koops, H. P. (1996).Phylogenetic diversity within the genus Nitrosomonas. Syst. Appl. Microbiol. 19, 344–351.
Prosser, J. I. (1989) Autotrophic nitrifiation in bacteria. Adv. Microbiol. Physiol. 30:125-181
Purkhold, U., Pommerening-Roser, A., Jureschko, S., Schemid, M. C., Koops, H. P., and Wanger, M. (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rDNA and amoA sequence analysis: implication for molecular diversity surveys. Appl. Environ. Microbiol. 66:5368-5382.
Purkhold, U., Wagner, M., Timmermann, G., Pommerening-Roser, A., and Koops, H. P. (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates:extension of the dataset and proposal of a new lineage within the nitrosomonads. International J. Syst. Evol. Microbiol. (2003), 53, 1485–1494
Quinlan A.V. (1986) Optimum Temperature Shift for Nitrobacter Winogradskyi. Wat. Res. Vol.20, No.5, pp. 611-617
Randall, C. W., Barnard, J. L., and Stensel, H. D. (1992). Design and retrofit of wastewater treatment plants for biological nutrient removal. Technomics Publishing, Inc.
Regan, J. M., Harrington, G. W., and Noguera, D. R. (2002) Ammonia- and nitrite-oxidizing bacterial communities in a pilot-scale chloraminated drinking water distribution system. Appl. Environ. Microbiol. 68, 73.
Regan, J. M., Harrington, G. W., Baribeau, H., Leon, R. D.,and Noguerab,D. R. (2003) Diversity of nitrifying bacteria in full-scale chloraminated distribution systems. Wat. Res. 37 (2003) 197–205.
Richardson, R. E., Bhupathiraju, V. K., Song, D. L., Goulet, T. A., and Alvarez-Choen, L. (2002) Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques, Environ. Sci. Technol. 36 2652-2662.
Rotthauwe, J., Witzel, K., and Liesack,W. (1997) The ammonia monooxgenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing population. Appl. Environ. Microbiol. 63:4704-4712.
Scala, D. J., and Kerkhof, L. J. (2000) Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis, Appl. Environ. Microbiol. 66 1980-1986.
Schoberl R. F., and Ahlert R.C. (1975) Kinetic Response of Pertur Bed Marine Nitrification Systems”, J. WPCF 47, pp.122-134
Schramm, A., Larsen,L. H., Revsbech, N. P., Ramsing, N. B., Amann, R., and Schleifer, K. H. (1996) Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes. Appl. Environ. Microbiol. 62: 4641–4647.
Shammas, N. K. (1986) Interactions of temperature, pH, and biomass on the nitrification process, J. WPCF. 58 (1): 52-59.
Shieh, W. K., and LaMotta, E. J. (1979) Effect of initial substrate concentration on the rate of nitrification in a batch experiment. Biotechnol. Bioengrg. 21 (1):201-211
Shuval, H. I. and Gruener, N. (1997) “Infant methemoglobinemia and other health effects of nitrate in drinker water”. Prog. Wat. Tech. 8:183-193.
Siyambalapitiya, N., Blackall, L. L. (2005) Discrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe for Gammaproteobacteria. FEMS Microbiol. Lett. 242 (2005) 367–373.
Sorensen H. B. (1993) “The removal of nitrogen compounds from wastewater”Elsevier, Denmark, pp153-165;215-216.
Stahl, D. A., Lane, D. J., Olsen, G. J., and Pace, N. R. (1985) Characterization of a Yellowstone hot spring microbial community by 5S ribosomal RNA sequences. Appl. Environ. Microbiol. 49, 1379-1384.
Stehr, G., Bottcher, B., Dittberner, P., Rath, G. and Koops, H. P.(1995). The ammonia-oxidizing nitrifying population of the River Elbe estuary. FEMS Microbiol. Ecol. 17, 177–186.
Stratton F. E. (1968), "Ammonia Nitrogen Losses from Streams",Journal of Sanitary Engineering Division, ASCE, Vol.94, No.SA6,p1085-1092.
Suwa, Y., Imamura, Y., Suzuki, T., Tashiro, T. & Urushigawa, Y. (1994). Ammonia-oxidizing bacteria with different sensitivities to (NH4)2SO4 in activated sludge. Wat. Res. 28, 1523–1532.
Suwa, Y., Sumino, T., and Noto, K. (1997) Phylogenetic relationships of activated sludges of ammonia oxidizers with different sensitivities to ammonium sulfate. J. General Appl. Microbiol. 43, 373.
Teske, A., Alm, E., Ragan, J. M., Rittman, B. E., and Stahl, D. A. (1994) Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176:6623-6630.
USEPA (1993) Manual: Nitrogen control. Cincinnati, OH.，pp.87-97
Van der Maarel, M. J. E. C., Artz, R. R. E., Haanstra, R., and Forney, L. J. (1998) Association of marine Archaea with the digestive tracts of two marine fish species, Appl. Environ. Microbiol. 64 2894-2898.
Versalovic, J., Koeuth, V., Mazurek, G. H., Whittam, T. S., Musser, J. M., and Lupski, J. R. (1995) DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction, Pathol Lab Meb Arch. 110 23-29.
Wagner, M., Rath, G., Amann, R., Koops, H. P., and Schleifer, K. H. (1995) In situ identification of ammonia-oxidizing bacteria. Syst. Appl. Microbiol. 18, 251.
Ward, B. B., and Carlucci, A. F. (1985) Marine ammonia- and nitrite-oxidizing bacteria: Serological diversity determined by immunofluorescent in culture and in environment. Appl. Environ. Microbiol. 50:194-201.
Watson, S. W., Bock, E., Harms, H., Koops, H. P., and Hooper, A. B. (1989) Nitrifying bacteria. In Bergey's Manual of Systematic Bacteriology, pp. 1808. Edited by J. T. Staley, M. P. Bryant, N. Pfenning & J. G. Holt. Baltimore: Williams & Wilkins.
Watts, J. E., Wu, Q., Schreier, S. B., May, H. D., and Sowers, K. R. (2001) Comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques. Environ. Microbiol. 3: 710-719
Woese, C. R., Weisburg, W. G., Paster, B. J., Hahn, C. M., Tanner,R. S., Krieg,N. R., Koops, H. P., Harm,H., and Stackebrandt, E.(1984) The phylogeny of the purple bacteria: the beta-subdivision. Syst. Appl. Microbiol. 5:327-336.
Zhu, S., and Chen, S. (1999) An experimental study on nitrification biofilm performance using a series reactor system, Aquacultural Engrg. 20:245-259.
行政院環境保護署 (2002) EPA-91-GE06-02-106 畜牧廢水污染防治措施提升計畫。
李澤民 (1994) 環境保護法規—公害防治部份，大學圖書供應社
沈元中 (1994) 不同處理方式影響高濃度硝酸鹽廢水生物脫硝效果之研究，國立中興大學環境工程學研究所碩士論文
周寬典譯 (1996) 養豬廢水處理之基本概念（下），現代畜殖，七月: 88-97
官政明、吳繼芳、羅中恆 (1994) 以SBR 去除豬糞尿污水中之氮磷及曝氣設備之評估，八十三年度畜牧污染防治試驗研究計畫成果報告彙編，行政院農業委員會及台灣省畜產試驗所，60-63。
林仁混 (1994) 飲用水中有毒氯化物, 亞硝基與硝基化合物之成因探討與去除方法之研究，行政院環保署
洪嘉謨、郭猛德 (2001) 豬糞尿處理與資源化，畜牧要覽養豬篇（增修版），第327 頁。中國畜牧學會編印，台北市。
洪嘉謨、蘇清全、郭猛德、林財旺、徐彩煥、李啟忠、沈韶儀 (1997) 三段式豬糞尿處理系統之評估-—放流水質與87 年環保標準比較（Ⅰ），畜產研究 30(4)：379-386。
張錦松及黃政賢主編 (1993) 環境工程概論，新科技書局。
郭瓊梅 (1996) 生物處理統去除都市污水中營養鹽之模擬分析，國立中興大學環境工程研究所碩士論文
曾四恭，曹明淅 (2003) 同槽硝化脫硝去除廢水氨氮之研究，國立台灣大學環境工程學研究所碩士論文
黃汝賢、李志源及陳瑞仁 (1993) 台灣地區豬糞尿廢水處理系統之功能評估（第一年計畫），八十二年度畜牧污染防治試驗研究計畫成果報告彙編。行政院農業委員會及台灣省畜產試驗所，121-132。
黃汝賢、紀長國、謝國強 (1998) 養豬廢水八十七年放流水標準之檢討與氮、磷去除技術之研究（II）II. 改良三段式法之設計流程使同時去除有機物、氮及磷，八十三年度畜牧污染防治試驗研究計畫成果報告彙編，行政院農業委員會及台灣省畜產試驗所，6-14。
黃汝賢、郭季華 (1998)三段式法處理後豬糞尿廢水之色度去除，畜產研究 31(1)：9-25
鄭幸雄，莊蕙萍 (2004) 三段式流體化床生物程序處理PAN 廢水之程序功
能評估與微生物族群動態變化之探討 ，國立成功大學環境工程研究所碩士論文。
鄭幸雄，彭欽鑫 (2004) 三段生物程序中好氧硝化槽功能評估
與分生檢測生態研究 ，國立成功大學環境工程研究所碩士論文。
聯合國環境規畫署、世界衛生組織合編 (1987) 硝酸鹽、亞硝酸鹽和N—亞硝基化合物，中國環境科學出版社。