臺灣博碩士論文加值系統

環境分子生物技術常應用基因定序法及核酸探針(nucleic acid probes)雜交法來分析微生物族群，但微生物偵測能力、實驗解析度、實驗操作難易度、所費時間及成本不盡相同。微陣列(microarray)技術是近五年在生命科學領域中迅速發展的新技術，透過微加工及微電子技術，在固體晶片表面上構建微型生化分析系統，其步驟包括︰探針設計、晶片製備、待測樣品製備、雜交反應和訊號分析等。本研究除收集國內外文獻發表之核酸探針外，另以生物資訊軟體設計出可檢測生物處理程序中微生物族群之核酸探針，用以製備微陣列晶片，並以實驗室規模生物處理程序最佳試程之活性污泥基因選殖株16S rDNA(ribosomal deoxyribonucleic acid, rDNA)序列作為晶片檢測標的物，最終以生物資訊軟體Vector NTI模擬晶片雜交結果，以確認微陣列晶片探針雜交反應之專一性，應用微陣列技術解析生物營養鹽去除程序污泥菌相。

Gene Sequencing and nucleic acid probes were used to analyze complicated microbial diversity in environmental science. The detectable ability, resolution, hardness, time required, and cost in aforementioned methods were distinct. The concepts of microarray technology including probe-designed, biochip construction, labeling of the detected sample, hybridization between detected sample and designed probes, and signal analysis in biochip were developed in life-science applications in recent five years. This study collected a lot of nucleic acid probes from published journal papers or bioimformatic databases on website. Furthermore, bioinformatics softwares were abapted to develop probes on microarray chip. The 16S rDNA clone sequences were collected form steady-state activated sludge in the laboratory-scale biological nutrient removal process. Eventually, the results demonstrated Vector NTI could simulate the hybridizations results. Moreover, simulation results of hybridization between designed probes and target DNA was the same as experimental results. Therefore, microarray technology could identify the microbial diversity in biological nutrient removal process by microarray technology.

誌謝 ------------------------------------------------------------------------i
中文摘要 ----------------------------------------------------------------ii
英文摘要 ----------------------------------------------------------------iii
目錄 ------------------------------------------------------------------------iv
表目錄 ------------------------------------------------------------------------v
圖目錄 ------------------------------------------------------------------------vi
第一章 緒論--------------------------------------------------------------------1
第一節 研究緣起----------------------------------------------------------------1
第二節 研究目的與內容----------------------------------------------------------2
第三節 研究架構----------------------------------------------------------------4
第二章 文獻回顧----------------------------------------------------------------5
第一節 生物營養鹽去除程序活性污泥菌相分析--------------------------------------5
一 生物除氮原理及菌相------------------------------------------------------7
二 生物除磷原理及除磷菌----------------------------------------------------10
三 污泥膨化與絲狀菌--------------------------------------------------------12
第二節 環境分子生物檢測技術----------------------------------------------------15
一 分子生物檢測技術之原理--------------------------------------------------15
二 分子生物檢測技術之應用及限制--------------------------------------------18
第三節 微陣列技術檢測原理及應用------------------------------------------------29
一 微陣列技術原理----------------------------------------------------------29
二 微陣列晶片製作----------------------------------------------------------32
三 微陣列晶片的應用--------------------------------------------------------33
第三章 研究方法----------------------------------------------------------------36
第一節 微陣列晶片設計與檢測方法------------------------------------------------37
一 探針設計----------------------------------------------------------------37
二 微陣列晶片的製備--------------------------------------------------------42
三 活性污泥之樣本標定與雜交反應--------------------------------------------44
四 清洗與呈色反應----------------------------------------------------------47
第二節 分子生物實驗方法--------------------------------------------------------49
一 16S rDNA萃取------------------------------------------------------------49
二 基因選殖----------------------------------------------------------------52
三 定序及親緣關係圖製作----------------------------------------------------54
四 生物資訊軟體模擬雜交反應------------------------------------------------55
第三節 基因選殖株來源----------------------------------------------------------56
一 缺氧-好氧生物除氮程序---------------------------------------------------56
二 厭氧及多段好氧-缺氧去氮除磷程序-----------------------------------------57
第四節 研究儀器與設備----------------------------------------------------------58
第四章 研究結果與討論----------------------------------------------------------60
第一節 探針研發與晶片製備結果--------------------------------------------------60
第二節 生物營養鹽去除程序菌相分析----------------------------------------------68
一 缺氧-好氧生物除氮程序之菌相分析-----------------------------------------68
二 厭氧及多段好氧-缺氧去氮除磷程序之菌相分析-------------------------------75
三 菌相綜合比較------------------------------------------------------------81
第三節 生物資訊軟體模擬雜交反應與微陣列晶片呈色結果----------------------------84
一 缺氧-好氧生物除氮程序之雜交模擬與呈色結果-------------------------------84
二 厭氧及多段好氧-缺氧去氮除磷程序之雜交模擬與呈色結果---------------------90
第四節 微陣列技術與基因選殖株分析其結果之比較----------------------------------94
第五節 污泥總16S DNA實測-------------------------------------------------------99
第五章 結論與建議--------------------------------------------------------------102
參考文獻------------------------------------------------------------------------107
附錄一 晶片探針ㄧ覽表----------------------------------------------------------114
附錄二 探針專一性驗證圖--------------------------------------------------------117

Acharya M, et al. 2007, "Genotyping of edwardsiella tarda isolated from freshwater fish
culture system", Comp Immunol Microbiol Infect Dis, Vol. 30, No. 1, pp.33-40
Aharoni A., et al. 2000, "Identification of the SAAT gene involved in strawberry flavor
biogenesis by use of DNA microarrays", Plant Cell, Vol. 12, pp.647-662
Aharoni A., et al. 2001, "DNA microarrays for functional plant genomics", Plant Mol. Biol.
Vol. 48, pp.99-118
Alexander Loy, et al. 2005, "16S rRNA gene-based oligonucleotide microarray for
environmental monitoring of the betaproteobacterial order Rhodocyclales", Appl Environ
Microbiol, Vol. 71, No. 3, pp.1373-1386.
Amachi S, et al. 2005, "Active transport and accumulation of iodide by newly isolated
marine bacteria", Appl. Envir. Microbiol, Vol. 71, No. 2, pp.741-745.
Amann R. I., et al. 1995, "Phylogenetic identification and in situ detection of individual
microbial cells without cultivation." Microbiol. Rev. Vol. 59,No 1, pp.143-169
Anderson R. C., et al. 2000, "A miniature integrated device for automated multistep
genetic assays", Nucleic Acids Res, Vol. 28, pp.60
Andrew J. McBain, et al. 2003, "Microbial characterization of biofilms in domestic
drains and the establishment of stable biofilm microcosms", Appl. Envir. Microbiol,
Vol. 69, pp.177-185
Atlas R. M., et al. 1992, "Molecular approaches for environmental monitoring and
microorganisms", BioTechniques, Vol. 12, No 5,pp. 706-717
Bernhard S., et al. 2001, " - and -Proteobacteria control the consumption and release of amino acids on lake snow aggregates ", Appl. Envir. Microbiol, Vol. 67, No 2, pp.632-645
Brummer. I. H. M., et al. 2004, “Diversity and seasonal changes of uncultured
planctomycetales in river biofilms”, Appl Envir. Microbiol, Vol. 70, No 9,
pp.5094–5101
Chaiet L., and F.J. Wolf, 1964, "The properties of streptavidin, a biotin-binding protein
produced by streptomycetes", Arch Biochem Biophys, Vol. 106, No. 20, pp.1-5
Cho J.C., and J.M. Tiedje, 2001, "Bacterial species determination from DNA-DNA
hybridization by using genome fragments and DNA microarrays", Appl Environ
Microbiol, Vol. 67, No. 8, pp.3677-3682
Chaiet L., and F.J. Wolf, 1964, "The properties of streptavidin, a biotin-binding protein produced by streptomycetes", Arch Biochem Biophys, Vol. 106, No. 20, pp.1-5
Crocetti G.R., et al. 2002, "Dentification of polyphosphate accumulating organisms and
design of 16S rRNA-directed probes for their detection and quantitation", Appl Environ
Microbiol, Vol. 66, No. 3, pp.1175–1182
Daims, H., et al. 2000, "Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in
biofilms from wastewater treatment plants: diversity and in situ physiology", Water Sci.
Technol, Vol.41, pp.85–90
Daims, H., et al. 2001, "In situ characterization of Nitrospira-like nitrite-oxidizing
bacteria active in wastewater treatment plants", Appl. Envir. Microbiol,, Vol.67,
pp.5273–5284
Debouck, C. and Goodfellow, P.N. 1999, "DNA microarrays in drug discovery
anddevelopment", Nat Genet. Vol.21, No.1, pp.48-50
Desantis T.Z., et al. 2005, "Rapid quantification and taxonomic classification of
environmental DNA from both prokaryotic and eukaryotic origins using a microarray",
FEMS Microbiology Letter, Vol. 245, No. 2, pp.271-278.
Eikelboom, D. H., and van Buijsen H. J. J. 1981, "Microscopic Sludge Investigation
Manual". Report No.A49a, TNO Research Institnte, Delft ,The Netherlands.
Eikelboom, D. H. 2000, "Process Control of Activated Sludge Plants by Microscopic
Investigation, 1st ed," IWA publishing, UK, pp43-84
Erhart, R., et al. 1997, "Development and use of fluorescent in situ hybridization probes for
the detection and identification of Microthrix parvicella in activated sludge", Syst. Appl.
Microbiol, Vol.20, pp.310-318
Fang, H. H., et al. 2002, "Characterization of an acetate-degrading sludge without
intracellular accumulation of polyphosphate and glycogen", Water Res. Vol.36, No.13,
pp.3211-3218
Franke-Whittle, et al. 2005, "Design and application of an oligonucleotide microarray for
the investigation of compost microbial communities", Journal of Microbiological
Methods, Vol. 62, No.1, pp.37-56
Gabor, E. M., et al. 2002, “Efficient recovery of environmental DNA for expression
cloning by indirect extraction methods,” Federation of European Microbiological
Societies Microbiology Ecology, Vol. 44, No. 2, pp.153-163
Gieseke, A., et al. 2001, "Community structure and activity dynamics of nitrifying bacteria
in a phosphate- removing biofilm", Appl. Envir. Microbiol,, Vol.67, pp.1351–1362
Giffel, M.C., et al. 1977, "Discrimination between Bacillus cereus and Bacillus
thuringiensis using specific DNA probes based on variable regions of 16S rRNA", FEMS
Microbiology Letters, Vol.146, No.1, pp. 47-51
Gregory L.G., 2003, "Characterization of a nitrate-respiring bacterial community using the
nitrate reductase gene (narG) as a functional marker", Microbiology, Vol. 149, No. 1,
pp.229-237
Hacia J. G., 1999, "Resequencing and mutational analysis using oligonucleotide
microarrays", Nat. Genet, Vol. 21, No.1, pp.42-47
Heylen, K., et al. 2006, "Cultivation of denitrifying bacteria: optimization of isolation
conditions and diversity study", Appl. Envir. Microbiol,, Vol. 72, No. 4, pp.2637-2643
Horz, H. P., et al. 2000, "Identification of major subgroups of ammonia-oxidizing bacteria
in environmental samples by T-RFLP analysis of amoA PCR products", Journal of
Microbiological Methods, Vol. 39, pp.197–204
Hovanec T. A, et al. 1998, "Nitrospira-like bacteria associated with nitrite oxidation in
freshwater aquaria", Appl. Envir. Microbiol, Vol. 64, pp.258–264
Hu, P., et al. 1991, "Effect of pH on fungal growth and bulking in laboratory activated
sludges", Res. J. Water Pollut.Control Fed. Vol. 63, pp.267-277
Jenkins, D., et al. 1993, "Manual on the causes and control of sludge bulking and
foaming, 2nd ed." Lewis Publisher, pp.75-82.
Juretschko S., et al. 2002, "The microbial community composition of a nitrifying
denitrifying acticated sludge from an industrial sewage treatment plant analyzed by the
full-cycle rRNA approach", Syst. Appl. Microbiol., Vol. 25, pp.84-99
Kawaharasaki M, et al. 1998, "Development and application of 16S rRNA-targeted
oligonucleotide probe for detection of phosphate-accumulating bacterium Microlunatus
phosphorus in the enhanced biological phosphorus removal process", Water Sci. Technol,
Vol.37, No. 4, pp.481–484
Kelly,K.M. and Chistoserdov,A.Y. 2001, "Phylogenetic analysis of the succession of
bacterial communities in the Great South Bay", FEMS Microbiol. Ecol., Vol. 35, No. 1,
pp.85-95.
Kloos, K., et al. 1995, "DNA-probing indicates the occurrence of denitrification and
nitrogen fixation genes in Hyphomicrobium. Distribution of denitrifying and nitrogen
fixing isolates of Hyphomicrobium in a sewage treatment plant", FEMS Microbiol Ecol,
Vol. 18, pp.205-213
Koike. I, and Hattori. A, 1975, "Growth tield of a denitrification bacterium, Pseudomonas
denitrificans, underaerobic and denitrifying conditions", J.Gen. Microbiology, Vol. 88,
pp.1-10.
Kurian, K. M., et al. 1999, "DNA chip technology", J. Pathol, Vol. 187, pp.267-271
Lane D.J., et al., 1985, "Rapid determination of 16S ribosomal RNA sequences for
phylogenetic analyses", Proc. Natl. Acad. Sci. Vol. 82, pp.6955.
Lau, A.O., et al. 1984, "Growth kinetics of Sphaerotilus natans and a floc former in pure
and dual continuous culture", J. Water Pollut. Control Fed, Vol. 56, pp.41-51
Layton, A.C., et al. 2000, "Quantification of hyphomicrobium populations in activated
wastewater treatment system as determined by 16S rRNA analysis", Appl. Environ.
Microbiol, Vol. 66, pp.1167-1174
Liu, J. K., et al. 1997, "The role of nitrogenase in a cyanide-degrading Klebsiella oxytoca
strain", Proc. Natl. Sci. Counc. Repub, Vol. 2, pp.37-42
Liyou, W. U., et al. 2001, "Development and evaluation of functional gene arrays for
detection of selected genes in the environment", Appl. Envir. Microbiol,, Vol. 67, No.
12, pp.5780-5790
Malik, A., et al. 2003, "Coaggregation among nonflocculating bacteria isolated from
activated sludge" Appl. Envir. Microbiol, Vol. 69, No.10, pp.6056-6063
Manz, W., et al. 1992, "Phylogenetic oligodeoxynucleotide probes for the major subclasses
of Proteobacteria: problems and solutions", System. Appl. Microbiol, Vol. 15,
pp.593-600
Manz W., et al. 1996, "Application of a suite of 16S rRNA-specific oligonucleotide probes
designed to investigate bacteria of the phylum cytophaga flavobacter bacteroides in the
natural environment", Microbiol, Vol. 142, pp.1097-1106
Maszenan, A.M., et al. 2000, "A fluorescently labeled r-RNA targeted probe for the in situ
detection of G-bacteria of the genus Amaricoccus in activated sludge", J. Appl.
Microbiol, Vol. 88, pp.826–835
McCaig, A. E., et al. 1994, "Molecular analysis enrichment cultures of marine oxidizers",
FEMS Micobiol. Lett, Vol. 120, pp.363-368
McTavish, H., et al. 1993, "Sequence of the gene coding for ammonia monooxygenase in
Nitrosomonas europaea", J. Bacteriol, Vol.175, pp.2436-2444
Meier, H, et al. 1999, "Specific oligonucleotide probes for in situ detection of a major
group of Gram-positive bacteria with low DNA G+C content", Syst. Appl. Microbiol,
Vol. 22, pp.186-96
Metcalf, and Eddy Inc. 2003, Wastewater Engineering: Treatment and Reuse, 4th,
McGraw-Hill Book Co., New York
Miyoshi, T., et al. 2005, "Phylogenetic characterization of 16S rRNA gene clones from
deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters",
Appl. Envir. Microbiol, Nol. 71, No. 2, pp.1084-1088
Mobarry, B. K, et al. 1996, "Phylogenetic probes for analyzing abundance and spatial
organization of nitrifying bacteria", Appl. Envir. Microbiol, Vol. 62, No. 6, pp. 2156–
2162
Neef, A., et al. 1996, “Population analysis in a denitrifying sand filter: conventional and in
situ identification of Paracoccus sp. in methanol-fed biofilms”, Appl. Environ.
Microbiol, Vol. 62, pp.4329–4339
Neef, A., et al. 1998, "Monitoring a widespread bacterial group: in situ detection of
planctomycetes with 16S rRNA targed probes", Microbiology, Vol. 144, pp. 3257–3266
Nikolay S., et al. 2004, "Multipathogen oligonucleotide microarray for environmental and
biodefense applications", Biosensors and Bioelectronics, Vol. 20, pp.684-698
Olsen G.J., ed al., 1987, "Microbial ecology and evolution: a ribosomal RNA approach",
Annu. Rev. Microbiol. Vol. 40, pp.337
Ogura, J., et al. 2006, "Purification, Characterization, and gene analysis of cellulose
(Cel8A) from Lysobacter sp.", Biosci. Biotechnol. Biochem. Vol. 70, No. 10,
pp.2420-2428
Park H.D., et al., 2002, "Molecular analysis of ammonia-oxidizing bacterial populations in
aerated-anoxic orbal processes", Water Sci Technol., Vol. 46, No. 1-2, pp.273-280
Pascal E. Saikaly, et al. 2005, "Use of 16S rRNA gene terminal restriction fragment
analysis to assess the impact of solids retention time on the bacterial diversity of
activated sludge", Appl. Envir. Microbiol, Vol. 71, pp.5814-5822
Paternoster S. F., et al. 2002, "A new method to extract nuclei from paraffin-embedded
tissue to study lymphomas using interphase fluorescence in situ hybridization", American
Journal of Pathology, Vol. 160, No. 6, pp.1967-1970
Peplies J., et al. 2006, "A DNA microarray platform based on direct detection of rRNA for
characterization of freshwater sediment-related prokaryotic communities", Appl Environ
Microbiol, Vol. 72, No. 7, pp.4829-4838
Pommering, R. A., et al. 1996, "Phylogenetic diversity within the genus
Nitrosomonas", System. Appl. Microbiol, Vol. 19, pp. 344–351
Rabus, R., et al. 1999, "Anaerobic utilization of alkylbenzenes and n-alkanes from crude
oil in an enrichment culture of denitrifying bacteria affiliating with the betasubclass of
Proteobacteria", Environ. Microbiol, Vol. 1, pp.145–157
Richard, M.G., et al. 1985, "The growth physiology of the filamentous organism type 021N
and its significance to activated sluge bilking", J. Water Pollut. Control Fed, Vol. 57,
pp.1152-1162
Rossello-mora, R. A., et al. 1995, "The abundance of Zoogloea ramigera in sewage
treatment plants", Appl. Envir. Microbiol, Vol. 61, pp.702–707
Sanguin H., et al. 2006, "Potential of a 16S rRNA-Based Taxonomic Microarray for
Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial
Communities", Appl. Envir. Microbiol, Vol. 72, No. 6, pp.4302-4312
Sezgin. M., et al. 1978, "A unified theory of filamentous activated sludge bulking", JWPCF, Vol. 50, No.2, pp.362-381.
Schauer, M. and Hahn, M. W., 2005, "Diversity and phylogenetic affiliations of
morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of
a broad spectrum of freshwater habitats", Appl. Envir. Microbiol, Vol. 71, No. 4,
pp.1931-1940
Schena M., D., et al. 1995, "Quantitative monitoring of geneexpression patterns with a
complementary DNA microarray". Science, Vol. 270, pp.467-470
Scherf. U., et al. 2000, "A gene expression database for the molecular pharmacology of
cancer", Nat. Genet, Vol. 24, pp. 236-244,
Schuppler M, et al. 1998, "In situ identification of nocardioform actinomycetes in activated
sludge using fluorescent rRNA-targeted oligonucleotide probes", Microbiology, Vol. 144,
No. 1, pp.249–259
Schauer M., and Hahn M.W., 2005. "Diversity and phylogenetic of morphologically
conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum
of freshwater habitats", Appl. Envir. Microbiol, Vol. 71, No. 4, pp.1931
Shabir A. Dar, et al. 2005,“Nested PCR-denaturing gradient gel electrophoresis
approach to determine the diversity of sulfate-reducing bacteria in complex
microbial communities”, Appl. Envir. Microbiol, Vol. 71, pp.2325-2330
Sharga, B. M., 1997, "Bacillus isolates as potential biocontrol agent against chocolate spot
on faba beans", Can. J. Microbiol, Vol. 43, pp.915-924
Sonia M. T., et al. 2004, "Evaluation of 50-mer oligonucleotide arrays for detecting
microbial populations in environmental samples", BioTechniques, Vol. 36, pp.664-675
Stefan J., et al. 2002, "The microbial community composition of a nitrifying-denitrifying
activated sludge from an industrial sewage treatment plant analyzed by the full-cycle
rRNA approach system", Biomedical and Life Sciences, Vol. 81, pp 665-680.
Taroncher O. G.., et al. 2003, "Oligonucleotide microarray for the study of functional
GeneDiversity in the nitrogen cycle in the environment", Appl. Envir. Microbiol, Vol.
69, No2, pp.1159-1171
Tiago I, et al. 2004, "Bacterial diversity in a nonsaline alkaline environment: Heterotrophic
aerobic populations", Appl. Envir. Microbiol, Vol.70, No.12, pp.7378-7387.
Tolli J, and King G.M., 2005, "Diversity and Structure of Bacterial Chemolithotrophic Communities in Pine Forest and Agroecosystem Soils", Appl. Envir. Microbiol, Vol. 71,
No. 12, pp.8411-8418.
Thomas E. Freitag., and James I., 2003, "Prosser community structure of
ammonia-oxidizing bacteria within anoxic marine sediments", Appl. Envir. Microbiol, Vol. 69, pp.1359-1371
Wagner M., et al. 1994, "Development of an rRNA-targeted oligonucleotide probe specific
for the genus Acinetobacter and its application for in situ monitoring in activated sludge",
Appl. Envir. Microbiol,, Vol. 60, No. 3, pp.792-800
Wagner, M., et al. 1995, "In situ identification of ammonia-oxidizing bacteria", Syst. Appl.
Microbiol, Vol. 18, pp.251-264
Wagner, M., et al. 1996, "In situ analysis of nitrifying bacteria in sewage treatment plants",
Water Sci. Technol, Vol. 34, pp.237–244
Wanner, J., 1994, "Activated sludge bulking and foaming control, 1st ed., Technomic
Publishing Co., Inc, Lancaster, USA, pp129-206.
Wagner M, et al., 2005, "Functional marker genes for identification of sulfate-reducing
prokaryotes", Methods Enzymol., Vol. 397, pp.469-89
Watanabe M, and Sasaki K, 1998, "Growth and flocculation of a marine photosynthetic
bacterium Rhodovulum sp.", [J]. Appl Microbiol Biotechnol, Vol. 50 , pp.682-691.
Wong, M.T., et al. 2004, "Identification and occurrence of tetrad-forming
Alphaproteobacteria in anaerobic: aerobic activated sludge processes", Microbiology,
Vol.150, pp.3741–3748
Young C.C., et al., 1998, "Characterization of the nitrogen fixation and ferric phosphate
solubilizing bacteria isolated from a Taiwan soil", Chinese Agri. Chemi. Soc., Vol. 36,
pp.201-210
李昱良，2004，Stenotrophomonas maltophilia多重抗藥性的研究，國立臺灣大學醫事技術學研究所，碩士論文。
洪志昌、陳亞雷，2006，"Bacterial community assessment of Burkholderia pseudomallei in cropped soil"，第11屆細菌學研討會論文集。
張裕釧、吳美貌，2005，"生物性肥料於有機農業發展上的重要性" 農業生技產業季刊，第四期，頁1-8
楊盛行，2005，"生物性肥料的開發與應用潛力"，農業生技產業季刊，第四期，頁9-17
何漣漪，2003，奧妙無窮的微生物世界，科學發展2003年，361期，頁49-53。
周裕然，2002，多段進流去氮除磷程序穩動態處理及控制特性之研究，國立中央大學環境工程研究所，博士論文。
周裕然等，2005，"活性污泥系統中脫硝菌分子生物檢測技術之探討-以微陣列技術為例"，第十七屆中華民國環境工程學會論文集，中壢。
林茗儀，2005，活性污泥脫硝基因及脫硝菌多樣性之研究，私立中原大學土木工程學系，碩士論文。
林秀萍，2004，蓮池潭紫色不含硫光合菌之分類與特性探討，國立中山大學生物科學系，碩士論文
馬立人，蔣中華， 2003， 生物晶片 ，二版，九州出版社。
張謝淵，2000，AOAO 污水處理程序去除營養鹽之特性研究，國立中央大學環境工程研究所，博士論文。
梁德明等，2001，"AICAR生物程序處理工業廢水案例研究"，2001產業環保工程實務研討會論文集。
梁德明等，2003，"活性污泥膨化與泡沫問題的診斷與防治案例研究"，2003產業環保工程實務研討會論文集。
陳健尉，2003，"生物晶片：技術發展及在生命科學上之應用"，後基因時代之生物技術，頁215~231。
陳睿斌，2001，應用分子生物技術進行生物處理程序菌相分析之研究，國立中央大學環境工程研究所，碩士論文。
曾怡禎，2001，"利用分子生物方法分析微生物社會的結構"，環境保護分子生物科技策略論壇資料集。
黃俊霖，2001，以分子生物技術探討厭氧生物產氫程序之菌群結構，國立中央大學環境工程研究所，碩士論文。
劉文佐，1999，"微生物辨識DNA 晶片"，科學月刊，頁726-731。
賴芳林，2002，"探討亞硝酸鹽的健康危害"，環境檢驗雙月刊，41期，頁4345。