石拓 教授、博导
Dr. SHI, Tuo
Professor of Marine Genomics and Biotechnology
tuoshi@sdu.edu.cn
实验室主页/Shi Lab Homepage:
http://faculty.sdu.edu.cn/shituo
教育/工作经历：
山东大学，教授、博导（2020–）
厦门大学，教授、博导（2015–2019）
美国蓝宝石能源（Sapphire Energy）公司，资深科学家（2013–2014）
美国奥奇能生物能源（Algenol Biofuels）公司，首席科学家（2008–2012）
加利福尼亚大学圣克鲁兹分校，博士后（2006–2008）（导师：Jonathan P. Zehr）
罗格斯, 新泽西州立大学，博士（2000–2006）（导师：Paul G. Falkowski）
Experiences:
Professor, Shandong University (2020–)
Professor, Xiamen University (2015–2019)
Senior Scientist, Sapphire Energy, Inc., USA (2013–2014)
Principal Scientist, Algenol Biofuels, Inc., USA (2008–2012)
Post-doctoral Scholar, University of California – Santa Cruz (2006–2008) (Advisor: Jonathan P. Zehr)
Ph.D., Rutgers, the State University of New Jersey (2000–2006) (Advisor: Paul G. Falkowski)
研究方向：
微型生物介导的关键生源要素循环；
珊瑚礁全球变化生物学；
藻类能源、化工与健康产品
Research Interests:
Microbes-mediated Key Element Cycles;
Coral Reef Global Change Biology;
Algal Fuels, Chemicals, and Health Products
代表性著作/Selected publications:
1. Shi T*, Niu G, Kvitt H, Zheng X*, Qin Q, Sun D, Ji Z, & Tchernov D. (2020). Untangling ITS2 genotypes of algal symbionts in zooxanthellate corals. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13250.
2. Muñoz-Marín MC, Shilova IN, Shi T, Farnelid H, Cabello AM, & Zehr JP. (2019). The transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium "Candidatus Atelocyanobacterium Thalassa" (UCYN-A). mBio 10: e02495-18. https://doi.org/10.1128/mBio.02495-18
3. Jiao K, Xiao W, Xu Y, Zeng X, Ho SH, Laws EA, Lu Y, Ling X, Shi T, Sun Y, Tang X, & Lin L. (2018). Using a trait-based approach to optimize mixotrophic growth of the red microalga Porphyridium purpureum towards fatty acid production. Biotechnology for Biofuels 11:273. https://doi.org/10.1186/s13068-018-1277-7
4. Chang J, Le K, Song X, Jiao K, Zeng X, Ling X, Shi T, Tang X, Sun Y, & Lin L. (2017). Scale-up cultivation enhanced arachidonic acid accumulation by red microalgae Porphyridium purpureum. Bioprocess and Biosystems Engineering 40: 1763–1773. https://doi.org/10.1007/s00449-017-1831-x
5. Shi T, Ilikchyan I, Rabouille S, & Zehr JP. (2010). Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH8501. The ISME Journal 4: 621–632. https://doi.org/10.1038/ismej.2009.148
6. Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, Bench SR, Moisander PH, Paerl RW, Tripp HJ, Montoya JP, Moran MA, & Zehr JP. (2009). In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. The ISME Journal 3: 618–631. https://doi.org/10.1038/ismej.2009.8
7. Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, Shi T, Tripp HJ, & Affourtit JP. (2008). Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Science 322: 1110–1112. https://doi.org/10.1126/science.1165340
8. Shi T, & Falkowski PG. (2008). Genome evolution in cyanobacteria: The stable core and the variable shell. Proceedings of the National Academy of Sciences of USA 105: 2510–2515. https://doi.org/10.1073/pnas.0711165105
9. Shi T, Sun Y, & Falkowski PG. (2007). Effects of iron limitation on the expression of metabolic genes in the marine cyanobacterium Trichodesmium erythraeum IMS101. Environmental Microbiology 9: 2945–2956. https://doi.org/10.1111/j.1462-2920.2007.01406.x
10. Shi T, Bibby TS, Jiang L, Irwin AJ, & Falkowski PG. (2005). Protein interactions limit the rate of evolution of photosynthetic genes in cyanobacteria. Molecular Biology and Evolution 22: 2179–2189. https://doi.org/10.1093/molbev/msi216
专利/Patents:
1. Wang K, Shi T, Piven I, Inaba M, Uliczka F, Kramer D, Enke H, Baier K, Friedrich A, Dühring U. Cyanobacterium sp. host cell and vector for production of chemical compounds in cyanobacterial cultures. 2018-Jan-9, USA, US 9,862,974 B2.
2. Dühring U, Baier K, Germer F, Shi T. Genetically enhanced cyanobacteria for the production of a first chemical compound harboring Zn2+, Co2+ or Ni2+-inducible promoters. 2017-Jan-24, USA, US 9,551,014 B2.
3. Wang K, Shi T. Shuttle vector capable of transforming multiple genera of cyanobacteria. 2016-Oct-25, USA, US 9,476,067 B2.
4. Piven I, Friedrich A, Dühring U, Uliczka F, Baier K, Inaba M, Shi T, Wang K; Enke H, Kramer D. Cyanobacterium sp. host cell and vector for production of chemical compounds in cyanobacterial cultures. 2016-Apr-19, USA, US 9,315,832 B2.
5. Piven I, Friedrich A, Dühring U, Uliczka F, Baier K, Inaba M, Shi T, Wang K, Enke H, Kramer D. Cyanobacterium sp. for production of compounds. 2015-Oct-13, USA, US 9,157,101 B2.
6. Wang K, Shi T, Piven I, Inaba M, Uliczka F, Kramer D, Enke H, Baier K, Friedrich A, Dühring U. Cyanobacterium sp. for production of compounds. 2014-Jun-26, WIPO, WO 2014/100799 A3
个人简介：
石拓，教授、博士生导师，2020年1月加盟山东大学。2006年毕业于美国罗格斯大学，获得生物海洋学博士学位，师从美国科学院院士、著名水境光合生物和海洋生态学家 Paul G. Falkowski。后在加州大学圣克鲁兹分校著名海洋微生物生态学家Jonathan P. Zehr实验室从事博士后研究两年。2015年至2019年以“福建省引进高层次人才”入聘厦门大学近海海洋环境科学国家重点实验室。此前在美国奥奇能生物能源公司、美国蓝宝石能源公司担任首席/资深科学家，领导利用藻类生产可持续生物燃料和高附加值化学品的商业化课题。在国际高水平期刊Science、PNAS、ISME J、mBio、Environ Microbiol、Mol Biol Evol等发表SCI论文数十篇，授权国际发明专利6项。主要研究方向为利用计算与实验生物学工具研究海洋微型生物对古代与现代海洋环境的适应，探索他们在生物地球化学循环（如碳、氮循环）中的作用。承担国家自然科学基金面上项目、国家自然科学基金中国-以色列合作项目、科技部国家重点研发计划项目等十余项科研项目。
Biography:
Prof. Shi joined SDU in 2020. He earned a Ph.D. in Paul Falkowski's lab at Rutgers University (2006), followed by a 2-yr Post-doctoral training on Marine Microbial Ecology at UC-Santa Cruz in Jon Zehr's lab. He was elected in an Overseas Outstanding Talents Recruitment Plan and joined the faculty of the State Key Laboratory of Marine Environmental Science at Xiamen University (2015-2019). Prior to this position, he spent 6 years (2008-2014) as Principal/Senior Scientist helping two U.S. biotech firms (Algenol Biofuels and Sapphire Energy) commercialize the use of algae to make sustainable biofuels and high-value green chemicals. Prof. Shi holds several US and WIPO patents and his work has been published in top journals including Science, PNAS, ISME J, mBio, Env Microbiol, and Mol Biol & Evol. The broad underlying theme of Prof. Shi's research is to integrate computational and experimental approaches to achieve a comprehensive understanding of how marine microbes affect, and are affected by, diverse oceanic environments, in both ancient and contemporary contexts.