課程資訊
課程名稱
珊瑚礁水域的有機物研究
Introduction to Methodologies and Recent Discoveries 
開課學期
105-2 
授課對象
理學院  海洋化學組  
授課教師
林卉婷 
課號
Ocean5104 
課程識別碼
241EU6010 
班次
 
學分
3.0 
全/半年
半年 
必/選修
選修 
上課時間
星期一2,3,4(9:10~12:10) 
上課地點
海研115 
備註
本課程以英語授課。
總人數上限:10人 
Ceiba 課程網頁
http://ceiba.ntu.edu.tw/1052Ocean5104_ 
課程簡介影片
 
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課程概述

This course is designed to guide students to learn about the organic matters in coral reef environment with a focus on the relatively overlooked dissolved organic matter. Coral reef ecosystem is highly productive and hosts a diverse community. To evaluate the sustainability of a reef ecosystem, we need to elucidate details on the organic nutrient cycling and thus such a research topic is emerging. During this course, we will go through recent discoveries on the biogeochemistry of the organic matter in reef waters around the world. We will also provide case studies to help students acquire analytical methods for characterizing organic matter. If funding is available, we will collect reef waters for hands-on practices. We will also conduct subsequent data analysis and interpretation to the environmental issues.
Each week, the course will start by me giving a brief introduction to the assigned topic. We will then spend 40 mins discussing recent published research papers relevant to the topic and another 30-40 mins to compile the data from the published research papers. We will then make our own data analysis and interpretations. Students will be required to write a minimum of five-page final report on reviewing or research report of related topics about coral reef organic geochemistry.  

課程目標
(1) Students will know about our current understanding of reef water organic geochemistry.
(2) Students will read many recently publications on reef water organic geochemistry.
(3) Students will present the compiled data and provide interpretations for the data.
(4) Students will identify challenges in research on organic geochemistry and seek for potential ways to overcome these challenges; compare with recently proposed research on tacking these challenges.
(5) At the end of the course, students will be able to think critically and present their thoughts clearly.
(6) Students will walk away from this course welcoming any questions about organic geochemistry in reef waters.
(7) Ultimate goal: students will become conscious about the cycling of organic matter in coral reef waters and have knowledge on methods for characterizing organic geochemistry.
 
課程要求
This course will be offered in English and thus, students must be able to understand English well enough to enroll. Students are required to read and present in English. This is a reading intensive course. Students are required to attend ALL classes. No more than two unexcused absences are permitted.  
預期每週課後學習時數
 
Office Hours
 
指定閱讀
1. O’Neil, J. M. and D. G. Capone (2008). Nitrogen cycling in coral reef environments. Nitrogen in the Marine Environment: 949-989.
2. Chen, Tzong‐Yueh, Jen‐Hua Tai, Chia‐Ying Ko, Chih‐Hao Hsieh, Chung‐Chi Chen, Nianzhi Jiao, Hong‐Bin Liu, and Fuh‐Kwo Shiah. (2016). Nutrient pulses driven by internal solitary waves enhance heterotrophic bacterial growth in the South China Sea. Environmental microbiology.
3. Tanaka, Y., et al. (2009). "Net release of dissolved organic matter by the scleractinian coral Acropora pulchra." Journal of Experimental Marine biology and ecology 377(2): 101-106.
4. De Goeij, J. M. and F. C. Van Duyl (2007). "Coral cavities are sinks of dissolved organic carbon (DOC)." Limnology and Oceanography 52(6): 2608-2617.
5. Nelson, C. E., et al. (2011). "Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem." The ISME journal 5(8): 1374-1387.
6. Wild, C., et al. (2008). "Biogeochemical responses following coral mass spawning on the Great Barrier Reef: pelagic–benthic coupling." Coral Reefs 27(1): 123-132.
7. Briggs, R., Padilla-Gamiño, J., Bidigare, R., Gates, R. and Ruttenberg, K. (2013) Impact of coral spawning on the biogeochemistry of a Hawaiian reef. Estuarine, Coastal and Shelf Science 134, 57-68.
8. Tarrant, A., Atkinson, M. and Atkinson, S. (2004) Effects of steroidal estrogens on coral growth and reproduction. Marine Ecology Progress Series 269, 121-129.
 
參考書目
Coral reefs: an ecosystem in transition (2012),
Edited by Zvy Dubinsky and Noga Stamblers
Digital version available through NTU library "http://link.springer.com/book/10.1007%2F978-94-007-0114-4"

Important chapters:
• Biogeochemistry of Nutrients by Marlin J. Atkinson
• The Role of Dissolved Organic Nitrogen (DON) in Coral Biology and Reef Ecology by Yoshimi Suzuki and Beatriz E. Casareto
• The Role of Plankton in Coral Trophodynamics by Christine Ferrier-Pagès, Mia Hoogenboom, and Fanny Houlbrèque
• Fish or Germs? Microbial Dynamics Associated with Changing Trophic Structures on Coral Reefs by Elizabeth A. Dinsdale and Forest Rohwer
 
評量方式
(僅供參考)
   
課程進度
週次
日期
單元主題
Week 1
2/20  Why is coral reef ecosystem important?
Why is the research on organic geochemistry of reef ecosystem important?
What is the difference between particulate organic matter (POM), dissolved organic matter (DOM), colloidal organic matter (COM) and suspended organic matter (SOM)?
Student presentation: Relevance of coral reef organic geochemistry to your research 
Week 2
2/27  No class. In observation of 228 Memorial Day.  
Week 3
3/09   ** NOTE: Time changed **
International conferences-
Why do we attend conferences?
What do we do during the conferences?
Attend talks, read posters, interact with researchers, discuss with collaborators, reach out and find potential new collaborators, mentor students,
(1) Webcast from ASLO meeting in Honolulu
ASLO:Association for the Sciences of Limnology and Oceanography
(2) Watch a conference talk and learn about organic C:N:P in coral ecosystems.
https://www.youtube.com/watch?v=mtL-TYRmhj0&index=23&list=PLO1PEYBjX6ZkXlWXEhjqkHYCQ8S24MRz1 
Week 4
3/20  Review of organic chemistry:
(1) Discuss about the talk by Dr. Mia Hoogenboom
(2) carbohydrates, proteins, peptides, amino acids, lipids and fatty acids, lignin, kerogen and colored-organic matter 
Week 5
3/27  Organic matters in coral reef ecosystems Assigned reading O’Neil, J. M. and D. G. Capone (2008)
(1) Sizes: from large ones to the tiny ones
(2) Locations: from seawater to coral reefs to reef sediments
(3) Producers: coral symbionts, phytoplankton, benthic primary producers, algae etc.
(4) Consumers: corals and others
(5) Sampling methods

**Nealson (1997) paper summarize the energetics of nitrogen redox states** 
Week 6
4/3  No class. Spring break. In observation of Tomb Sweeping Day; Women and Children's Day 
Week 7
4/10  Dynamics of dissolved organic matter and biological activities in coral reef waters: the importance of physical forcing. A case study from Taiwan’s DongSha Atoll (Assigned reading: Chen et al. 2016).  
Week 8
4/17  Coral is a source of DOM? (Assigned reading: Takana et al. 2009). 
Week 9
4/24  Coral is a sink of DOM?
Assigned reading:
1.De Goeij, J. M. and F. C. Van Duyl, 2008;
2. Nelson et al. 2011 
Week 10
5/1  All about sampling
Biological samples- large ones and microscopic ones
Dissolved organic samples
What can we use? What can't we use? Why?
How to sample? Snorkel? Scuba dive?
How to preserve samples?  
Week 11
5/12  Field trip to Northeast Taiwan to observe the dynamics of a coral reef environment (tentative site: 鼻頭角地質公園) 
Week 12
5/15  Roles of dissolved organic matter in coral reef ecosystems? (I-case study/lab)
Reactivity of DOM in marine environment: labile versus refractory; degradation and preservation; young versus old. How to apply the known knowledge from other marine environments to coral reef ecosystems?  
Week 13
5/22  Roles of dissolved organic matter in coral reef ecosystems? (II-case study/lab)
Reactivity of DOM in marine environment-amino acid compositional analysis using high performance liquid chromatography  
Week 14
5/29 (端午節)  Roles of dissolved organic matter in coral reef ecosystems? (III-case study/lab)
Reactivity of DOM in marine environment-incubation to observe degradation of reef water DOM
 
Week 15
6/5  DOM and coral spawning-I (Assigned reading: Wild et al. 2008 (Chao-Yuan present) ; Briggs et al. 2013 (Emma present); Tarrant et al. 2004 (Tina present))  
Week 17
6/12  Final review or research report