20 世紀初，石油的量產造就了人類文明的繁榮。然而由於石油產品的運送、廢棄物處理等因素，使得油類污染成為環境保護的重大議題; 另一方面則是重金屬汙染，人類採礦的歷史相當悠久，像是金銀銅等重金屬，隨著開採範圍擴大，汙染範圍也隨之擴大，在河流、土壤等環境，都能發現重金屬的痕跡。台灣歷史上也有許多的重金屬汙染事件，例如RCA汙染事件或者是中石化在台南四草造成的戴奧辛以及汞汙染。對於環境的污染，動物能選擇遷徙，但是植物與微生物卻無法逃走。在逆境之下，植物與微生物利用不同的生理代謝機制，吸收或降解這些有毒物質，讓細胞或植物體免於毒害，這些議題在科學界已經討論許久。許多研究鑑定出許多相關基因能降解油汙或者是重金屬。隨者基因體科技的快速發展，更能了解在污染物中微生物組成為何。本篇研究從物種多樣性指數來切入，植物根際菌相的物種多樣性高於汙染土壤，且兩種汙染物的物種多樣性分析有顯著差異 ; 從土壤核心微生物組成來作探討，變形菌門 (Proteobacteria)、擬桿菌門 (Bacteroidetes)為油汙汙染的主要組成，變形菌門以及放線菌門 (Actinobacteria)為重金屬汙染的主要組成 ; 藉由土壤獨特微生物組成分析發現，油汙土的厚壁菌門 (Firmicutes)以及軟壁菌門 (Tenericutes)佔比高於重金屬汙染土 ; 從血桐以及五節芒根際土的分析中發現，變形菌門、放線菌門是兩種植物根際核心微生物群的主要組成，另外在根際土獨特微生物相發現到血桐的酸桿菌門 (Acidobacteria)佔比高於五節芒。以上結果發現到不同汙染源有其獨特微生物相，而不同植物生長於汙染地則具有相似的核心微生物組成。本篇論文利用多源基因體學深入探討其中的奧秘，希望能尋找降解汙染源的最好方法。

Since the 20th century, the production of petroleum created an unprecedented prosperity of human civilization. However, due to factors such as transportation and disposal, oil pollution has become a major issue in environmental protection. On the other hand, heavy metal pollution has a long history of human mining. Heavy metals include gold, silver and copper. As the mining area expands, the pollution area also increases. In Taiwan, many heavy metal pollution events in history, such as the RCA pollution. For escaping environmental pollution, animals can leave and find new lands, but plants and microorganisms cannot freely move. In the face of adversity, plants and microorganisms use different bio-metabolism mechanisms to absorb or degrade these toxic substances and protect cells or plants from toxicity. With the rapid development of genomic technology, we are able to study the microbial composition in environment which has pollutants. In this study, I focus on two kinds of contaminated soil, petroleum and heavy metal, and investigate the bacterial community with targeted Metagenomics by 16S rRNA gene. I found that Proteobacteria and Bacteroidetes are the main components of bacterial community in petroleum-polluted soil. Proteobacteria and Actinobacteria are the main components of bacterial community at the site with heavy metal pollution. According to the analysis of specific microbiome, the proportion of Firmicutes and Tenericutes in petroleum-polluted soil is higher than heavy metal contaminated soil. In Macaranga tanarius and Miscanthus floridulus rhizosphere, Proteobacteria and Actinomycetes are the main components of the core microbiome of the two plants. The above results shows that in different polluted area has their own specific microbial community, and different kinds of plants grow in contaminated soil share with similar core microbiome. This thesis uses metagenomics to explore more deeply, hoping to find the best way to degrade pollutants and protect the earth.

Amann, R. I., et al. "Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation." Microbiological Reviews 59(1): 143-169. (1995).
Andrades-Moreno L, Del Castillo I, Parra R, et al. "Prospecting metal-resistant plant-growth promoting rhizobacteria for rhizoremediation of metal contaminated estuaries using Spartina densiflora [J]." Environmental Science and Pollution Research, 21(5): 3713-3721. (2014).
Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A. C., Cruz, J. A., . . . Wishart, D. S. "METAGENassist: a comprehensive web server for comparative metagenomics." Nucleic Acids Research, 40(W1), W88-W95. (2012).
Belimov A A, Puhalsky I V, Safronova V I, et al. "Geochemical behavior of heavy metals in a Zn-Pb-Cu mining area in the State of Mexico (central Mexico) [J]." Environmental Monitoring and Assessment, 155(1-4): 355-72. (2009).
Burr T S, Schroth M N. Suslow T. "Increased potato yield by treatment of seed pieces with specific strains of Pseudomonas fluorescens and P. putida [J]." Phytopathology, 68(9): 1377-1383. (1978).
Cheng, W. X. "Rhizosphere priming effect: Its functional relationships with microbial turnover, evapotranspiration, and C-N budgets." Soil Biology & Biochemistry 41(9): 1795-1801. (2009).
Dong, Y. R., et al. "Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats." Astrobiology: 17. (2019).
Doornbos, R. F., et al. "Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review." Agronomy for Sustainable Development 32(1): 227-243. (2012).
Dos Santos, H. F., et al. "Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota." Scientific Reports 5: 11. (2015).
Drzyzga, O., Navarro J.M., Fernandez de las Heras, L., Garcia Fernandez, E., and Perera, J. "Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge." Int. J. Syst. Evol. Microbiol ; 59:1011-1015. (2009).
Ghori, Z., et al. "Chapter 15 - Phytoextraction: The Use of Plants to Remove Heavy Metals from Soil. " Plant Metal Interaction. P. Ahmad, Elsevier: 385-409. (2016).
Gilbert N, Fulthorpe R, Kirkwood A E. "Microbial diversity, tolerance, and biodegradation potential of urban wetlands with different input regimes [J]." Canadian Journal of Microbiology, 58(7): 887-897. (2012).
Glick B R. "Using soil bacteria to facilitate phytoremediation." Biotechnology Advances, 28(3):367 – 374. (2010).
Guo J, Tang S, Ju X, et al. "Effects of inoculation of a plant growth promoting rhizobacterium Burkholderia sp. D54 on plant growth and metal uptake by a hyperaccumulator Sedum alfredii hance grown on multiple metal contaminated soil [J]." World Journal of Microbiology and Biotechnology, 27(12): 2835-2844. (2011).
Hackstadt, A. J. and A. M. Hess. "Filtering for increased power for microarray data analysis." Bmc Bioinformatics 10: 12. (2009).
Handelsman, J., et al. "Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products." Chemistry & Biology 5(10): R245-R249. (1998).
Huang, C. L., et al. "Deciphering mycorrhizal fungi in cultivated Phalaenopsis microbiome with next-generation sequencing of multiple barcodes." Fungal Diversity 66(1): 77-88. (2014).
Ichor, T., et al. "Biodegradation of total petroleum hydrocarbon by aerobic heterotrophic bacteria isolated from crude oil contaminated brackish waters of bodo creek." J Bioremed Biodeg 5(5): 1. (2014).
Igwo-Ezikpe, M., et al. "Evaluation of Alcaligenes faecalis degradation of chrysene and diesel oil with concomitant production of biosurfactant." Research Journal of Environmental Toxicology 3(4): 159-169. (2009).
Ikuesan, F. A., et al. "The microbiological and physicochemical properties of some crude oil contaminated and uncontaminated agricultural soils in Ondo State, Nigeria." Pyrex Journal of Microbiology and Biotechnology Research 2(1): 1-8. (2016).
Kasemodel, M. C., et al. "Potentially toxic metal contamination and microbial community analysis in an abandoned Pb and Zn mining waste deposit." Science of the Total Environment 675: 367-379. (2019).
Khan S, Cao Q, Zheng Y M, et al. "Health risks of heavy metals in contaminated soils and food crops irrigated with wastewater in Beijing, China [J]." Environmental Pollution, 152(3): 686-92. (2008).
Koberl, M., et al. "Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health." Plos One 6(9): 9. (2011).
Lee M.D., J.M. Thomas, R.C. Borden, P.B. Bedient, J.T. Wilson,and C.H. Ward. "Biorestoration of aquifers contaminated with organic compounds." Crit. Rev Environ. Control, Vol. 18, pp.29-89. (1998).
Liao, W.-Z., et al. "A case study of heavy metal pollution site using phytoremediation technology." 14. (2017).
Macnaughton, S. J., Stephen, J. R., Venosa, A. D., Davis, G. A., Chang, Y. J., & White, D. C. "Microbial population changes during bioremediation of an experimental oil spill. " Applied and Environmental Microbiology, 65(8), 3566-3574. (1999).
Marschner, H., et al. "Root-induced changes in the rhizosphere - importance for the mineral-nutrition of plants." Journal of Plant Nutrition and Soil Science 149(4): 441-456. (1986).
Masindi, V. and K. Muedi. "Environmental contamination by heavy metals." (2018).
Ortas, I. "Determination of the extent of rhizosphere soil." Communications in Soil Science and Plant Analysis 28(19-20): 1767-1776. (1997).
Panke-Buisse, K., et al. "Selection on soil microbiomes reveals reproducible impacts on plant function." Isme Journal 9(4): 980-989. (2015).
Salt, D. E., et al. "Phytoremediation - A novel strategy for the removal of toxic metals from the environment using plants." Bio-Technology 13(5): 468-474. (1995).
Savolainen, V., et al. "Towards writing the encyclopaedia of life: an introduction to DNA barcoding." Philosophical Transactions of the Royal Society B-Biological Sciences 360(1462): 1805-1811. (2005).
Shahi, A., et al. "Reconstruction of bacterial community structure and variation for enhanced petroleum hydrocarbons degradation through biostimulation of oil contaminated soil." Chemical Engineering Journal 306: 60-66. (2016).
Shi, W., et al. "Isolation and characterization of novel bacterial taxa from extreme alkali-saline soil." World Journal of Microbiology & Biotechnology 28(5): 2147- 2157. (2012).
Singh, O. V. and R. K. Jain. "Phytoremediation of toxic aromatic pollutants from soil." Applied Microbiology and Biotechnology 63(2): 128-135. (2003)
Singh, S. N. and R. D. Tripathi. "Environmental bioremediation technologies." Springer Science & Business Media. (2007)
Sylvia Adipah. "Introduction of Petroleum Hydrocarbons Contaminants and its Human Effects. " Journal of Environmental Science and Public Health 3: 001-009. (2019).
Tang, C. S., et al. "Evaluation of agriculture-based phytoremediation in pacific island ecosystems using trisector planters." International Journal of Phytoremediation 6(1): 17-33. (2004).
Thomas, J., Lee, M., Bedient, P., Borden, R., & Canter, L. J. F. R., May-Oct. Rice Univ., Houston, TX. "Leaking underground storage tanks: remediation with emphasis on in situ biorestoration." RSKERI, Publication EPA600-287-008. (1987).
Todd, G. D., et al. "Toxicological profile for total petroleum hydrocarbons (TPH)." Agency for Toxic Substances and Disease Registry. (1999).
Turnbaugh, P. J. and J. I. Gordon. "An invitation to the marriage of metagenomics and metabolomics." Cell 134(5): 708-713. (2008).
Wang, Y. and P. Y. Qian. "Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in Metagenomic studies."Plos One 4(10): 9. (2009).
Watts, G. S., et al. "16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria." Journal of Applied Microbiology 123(6): 1584-1596. (2017).
Wokem, V. C., et al. "Isolation and characterization of hydrocarbon-utilizing bacteria from petroleum sludge samples obtained from crude oil processing facility in Nigeria." Journal of Applied Sciences and Environmental Management 21(2): 355-369. (2017).
Wu, G., et al. "A critical review on the bio-removal of hazardous heavy metals from contaminated soils: Issues, progress, eco-environmental concerns and opportunities." Journal of Hazardous Materials 174(1-3): 1-8. (2010).
Yateem, A., et al. "Investigation of microbes in the rhizosphere of selected grasses for rhizoremediation of hydrocarbon-contaminated soils." Journal Soil and Sediment Contamination 16(3): 269-280. (2007).
Zeng M, Liao B H, Lei M, Zhang Y, Zeng Q R, Ouyang B. "Arsenic removal from contaminated soil using phosphoric acid and phosphate." Journal of Environmental Science, 20(1):75 - 80. (2008).
Zhang Yan, Deng Yang-wu, Luo Xian-ping, Zhou Meng. "On soil contamination by heavy metal and microbial remediation technology[J]." Nonferrous Metals Science and Engineering, 3(1): 63-66.DOI: 10.13264/j.cnki.ysjskx.2012.01.001. (2012).