污水、固废处理处置的微生物过程研究

生物能源、污染场地生物修复的微生物资源开发和基因工程改造

2003 年在美国爱因斯坦医学院获微生物学博士学位后开始进入环境微生物学领域。2003-2010年，在美国橡树岭国家实验室系统开展了可用于污染环境生物清理和生物能源的环境微生物基因组学和基因工程学的研究。在此期间，作为科研项目负责人（PI）领导了一个由博士后、技术员和交换学生组成的实验室，并任美国能源部生物能源中心微生物基因工程课题负责人。与美国工程院院士James Liao 教授作为联合团队共同负责人，制造了世界上第一个纤维素-异丁醇转化细菌（该类细菌在自然界尚未发现），该项成就于2011 年3 月获时任美国能源部部长朱棣文的书面肯定，并被白宫网站和数十家国际媒体报道。

2010年9月全职回国，致力于通过基因组学和基因工程技术来研究气候变化对我国土壤微生物多样性的影响，建立了以基因组学和基因工程学为主要技术手段，以微生物为研究对象，以关键环境问题的基础科研为特色的研究思路，取得了一系列具有一定创新性和国际影响的研究成果，在The ISME Journal（《自然》出版集团刊物）、Global change biology、Environmental microbiolgoy等期刊发表多篇学术论文。2012 年以来获国家自然科学基金委面上、重点项目、科技部973、863等项目、住建部水专项等项目资助。2013年获“清华大学环境学院科研先进个人”荣誉，2014年获清华大学青年学者最高奖“学术新人奖”。

近年主持或者参与主持的科研项目：

1.海南国家公园研究院，基于微生物的海南热带雨林碳排放评估与调控，2023/04-2025/12，主持

2. 国家自然科学基金委，重点国际(地区)合作研究项目，养分添加对全球草地土壤微生物多样性和功能的影响及机理， 2021/10-2026/09，主持

3. 国家科学技术部，基于监测的污染物自然衰减新型指标体系与衰减效率评估方法，2020/01-2023/12，主持

4. 国家自然科学基金委，国家级人才项目，土壤微生物学，2019/01-2023/12，主持

5. 国家科学技术部，第二次青藏高原综合科学考察课题，高原土壤微生物多样性特征，2019/01-2023/12，主持

6. 城市污水高含固污泥高效厌氧消化装备开发与工程示范子课题（住建部水专项，2013-2016）

7. 碳循环关键过程及其与气候系统耦合的研究子课题（科技部973项目，2013-2017）

8. 冻土带天然气水合物微生物勘查技术子课题（科技部863项目，2012-2015）

9. 环境多因子对温带草原土壤微生物群落结构的影响（国家基金委面上项目，2012-2015）

10. 基于宏基因组学技术的工程系统微生物群落特征研究（国家重点实验室自主项目，2011-2013）

11.能源部生物能源中心梭菌遗传工程项目（美国能源部GTL项目, 2007 – 2012）

12. 杨树–微生物相互作用项目，分离微生物和遗传工程开发子课题（美国能源部GTL项目2009 – 2012）

13. 土壤微生物分布、转移过程中细胞胶结的定量分析子课题 (美国能源部ERSP exploratory项目2010 – 2011)

14.对重金属污染的地下水中分离和筛选功能微生物项目，分离微生物子课题（美国能源部ERSP项目，2007 – 2010）

15. 系统生物学方法理解植物抗旱性机理项目，功能基因组学分析和生物网络构建子课题（美国橡树岭国家实验室LDRD项目，2007 – 2010）

16. 合成气-醇类转换细菌的遗传工程开发（美国橡树岭国家实验室LDRD项目，2007 – 2010）

17. 食品生产过程中检测沙门氏菌的新型技术（Mars, Inc. 资助项目和美国橡树岭国家实验室Seed money项目2009 – 2010）

18. Shewanella Federation 还原金属分子机制子课题（美国能源部GTL项目，2006 – 2008）

19. 生物能源梭菌的遗传工程开发（美国橡树岭国家实验室Seed money项目, 2006 – 2007）

1.第16届中国土壤学会科学技术奖一等奖（2021）

2.清华大学 “学术新人”奖（2014）

3.清华大学环境学院科研先进个人(2013)

5.2018年8月3日，根据《国家杰出青年科学基金项目管理办法》的有关规定，国家自然科学基金委员会将2018年度国家杰出青年科学基金建议资助项目申请人名单予以公布，杨云锋在名单之中。

发表文章

近五年论文引用次数800余次。

1.M. Zhao, K. Xue, F. Wang, S. Liu, S. Bai, B. Sun, J. Zhou and Y. Yang* (2014), Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping, The ISME Journal, doi: 10.1038/ismej.2014.46

2.S Liu, F Wang, K Xue, B Sun, Y Zhang, Z He, JD Van Nostrand, J Zhou, Y Yang* (2014), The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry, Environmental Microbiology, doi:10.1111/1462-2920.12398

3.H Chu, S Wang, H Yue, Q Lin, Y Hu, X Li, J Zhou, Y Yang* (2014), Contrasting soil microbial community functional structures in two major landscapes of the Tibetan alpine meadow, MicrobiologyOpen, accepted

4.Y Gao, S Wang, D Xu, H Yu, L Wu, Q Lin, Y Hu, X Li, Z He, Y Deng, J Zhou, Y Yang* (2014), GeoChip as a Metagenomics Tool to Analyze the Microbial Gene Diversity along an Elevation Gradient, Genomics Data, accepted

5.M Zhao, F Wang, Shanshan Liu, K Xue, Y Liang, S Bai, Z He, JDV Nostrand, J Zhou, Y Yang*, B Sun* (2014), GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping, Genomics Data, accepted

6.Y. Sun, Y. Shen, P. Liang, J. Zhou, Y. Yang*, Xia Huang* (2014), The remarkable linkages between microbial functional potentials and wastewater constituents in large-scale operational membrane bioreactors for the municipal wastewater treatment, Water research 56, 162-171

7.Y Yang*, Y Gao, S Wang, D Xu, H Yu, L Wu, Q Lin, Y Hu, X Li, Z He, Y Deng, J Zhou (2014), The microbial gene diversity along an elevation gradient of the Tibetan grassland, The ISME Journal 8 (2), 430-440

8.J. Zhou, Y. Deng, P. Zhang, K. Xue, Y. Liang, JDV Nostrand, Y. Yang, Z. He, L. Wu, D. Stahl, T. Hazen, J. Tiedje, A. Arkin (2014), Stochasticity, succession, and environmental perturbations in a fluidic ecosystem, Proceedings of the National Academy of Sciences 111 (9), E836-E845

9.X Wang, Y Xia, X Wen, Y Yang, J Zhou (2014), Microbial Community Functional Structures in Wastewater Treatment Plants as Characterized by GeoChip, PLoS One 9(3): e93422

10.Y Zhang, J Cong, H Lu, C Yang, Y Yang, J Zhou, D Li (2014), An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types, PLoS One 9(4): e93773

11.Y Li, T Xu, T Tschaplinski, N Engle, Y Yang, D Graham, Z He, J Zhou (2014), Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation, Biotechnology for Biofuels 7 (1), 25

12.Y Xia, X Wang, X Wen, K Ding, J Zhou, Y Yang, Y Zhang (2014), Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors, Appl. Microbiol. Biotechnol, accepted.

13.Y Yang*, J Chen, D Qiu, J Zhou (2013), Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction, BMC microbiology 13 (1), 267

14.X Sun, Y Gao and Y Yang* (2013), Recent advancement in microbial environmental research using metagenomics tools,Biodiversity Science, 21 (4): 393–400

15.Y Yang* (2013), Omics breakthroughs for environmental microbiology, Microbiology China 40 (1), 18-33

16.Y Yang*, L. Wu, Q. Lin, M. Yuan, D. Xu, H. Yu, Y. Hu, J. Duan, X. Li, Z. He, K. Xue, J. Nostrand, S. Wang and J. Zhou (2013), Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland, Global Change Biology 19(2), 637–648

17.D Qiu, H Wei, Q Tu, Y Yang, M Xie, J Chen, MH Pinkerton, Y Liang, Z He, J Zhou (2013) Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1, Applied and environmental microbiology 79 (17), 5250-5257

18.G Mohr, W Hong, J Zhang, G Cui, Y Yang, Q Cui, Y Liu and AM Lambowitz (2013), A Targetron System for Gene Targeting in Thermophiles and Its Application in Clostridium thermocellum, PloS one 8 (7), e69032

19.J Zhou, Y Jiang, Y Deng, Z Shi, B Zhou, K Xue, L Wu, Z He and Y Yang (2013), Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities, mBio 4 (3)

20.J Zhou, W Liu, Y Deng, YH Jiang, K Xue, Z He, JD Van Nostrand, L Wu, Y Yang and A. Wang (2013), Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community, mBio 4 (2)

21.Y Zhang, Z Lu, S Liu, Y Yang, Z He, Z Ren, J Zhou and D Li (2013), Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau, BMC microbiology 13 (1), 72

22.Y. Deng, Y. Jiang, Y. Yang, Z. He, F. Luo and J. Zhou (2012), Molecular ecological network analyses, BMC Bioinformatics 13:113

23.Y. Li, T. Tschaplinski, N. Engle, C. Hamilton, M. Rodriguez, J. Liao, C. Schadt, A. Guss, Y. Yang and D. Graham (2012), Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations, Biotechnology for Biofuels 5:2-2

24.J Lin, J Zuo, R Ji, X Chen, F Liu, K Wang, Y Yang (2012), Methanogenic community dynamics in anaerobic co-digestion of fruit and vegetable waste and food waste, Journal of Environmental Sciences 24 (7), 1288-1294

25.J. Zhou, L. Wu, Y. Deng, X. Zhi, Y. Jiang, Q. Tu, J. Xie, J. D. Van Nostrand, Z. He and Y. Yang (2011), Reproducibility and Quantitation of Amplicon Sequencing-based Detection. The ISME Journal 5: 1303-1313

26.W. Higashide, Y. Li, Y. Yang and J. Liao (2011), Metabolic Engineering of Clostridium cellulolyticum for Production of Isobutanol from Cellulose, Applied and Environmental Microbiology 77(8): 2727-2733

27.J. Zhou, Y. Deng, F. Luo, Z. He and Y. Yang (2011) Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2, mBio 2(4): e00122-11

28.Y. Yang*, L. A. McCue, A. B. Parsons, S. Feng and J. Zhou (2010), The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control. BMC Microbiology 10:264

29.C. Hemme, Y. Yang, J. Zhou et al., Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production (2010). J. Bacteriol. 192(24): 6494-6496

30.H. Gao, S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K. Nealson, J. Fredrickson, J. Tiedje, M. Romine, J. Zhou (2010), Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration, Microbial Biotechnology 3(4): 455-466

31.X. Zhang, Z. Zhang, Z. Zhu, N. Sathitsuksanoh, Y. Yang and P. Zhang (2010), A Highly-Active Family 48 Cellobiohydrolase from Clostridium phytofermentans ISDg: Heterologous Expression in Escherichia coli and Bacillus subtilis, Characterization, and Processivity. Appl. Microbiol. Biotechnol 86(2):525-533

32.Y. Yang*, D. P. Harris, F. Luo, W. Xiong, M. Joachimiak, L. Wu, P. Dehal, J. Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin and J. Zhou (2009), Snapshot of Iron Response in Shewanella oneidensis by Gene Network Reconstruction, BMC Genomics 10:131

33.Y. Yang* (2009) Use of Genomic DNA as Reference in DNA Microarrays, Micro and Nano Technologies in Bioanalysis, 439-450

34.Y. Yang*, M. Zhu, L. Wu and J. Zhou (2008) Assessment of Data Processing to Improve Reliability of Microarray Experiments Using Genomic DNA Reference, BMC Genomics 9(S2):S5.

35.Y. Yang*, D. P. Harris, F. Luo, L. Wu, A. B. Parsons, A. V. Palumbo and J. Zhou (2008) Physiological and Transcriptomic Analyses to Characterize the Function of Fur and Iron Response in Shewanella oneidensis, BMC Genomics 9(S1):S11.

36.F. Luo, Y. Yang, J. Zhong, H. Gao, L. Khan, D. K. Thompson and J. Zhou (2007) Constructing Gene Co-expression Networks and Predicting Functions of Unknown Genes by Random Matrix Theory, BMC Bioinformatics 8:299. (co-first author)

37.F. Luo, Y. Yang, C. Chen, R. Chang, J. Zhou and R. Scheuermann (2007) Modular Organization of Protein Interaction Networks, Bioinformatics 23(2):207-214.

38.Y. Yang*, M. Zhu, L Wu, J Zhou (2007) Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays, Bioinformatics and Bioengineering 7: 593-600

39.M. Zhu, Q. Wu, Y. Yang and J. Zhou (2006) A New Approach to Identify Functional Modules Using Random Matrix Theory, Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 1:117-123.