Dr. Cheng Lei

Researcher and Doctoral Supervisor
Biogas Institute Ministry of Agriculture and Rural affairs
Chief Scientist of the "Anaerobic Microbial Technology Innovation Team" at the Chinese Academy of Agricultural Sciences
Recipient of the National Distinguished Young Scientist Fund (2023)
Academic and Technical Leader of Sichuan Province (2022)
Email: chenglei@caas.cn

Education

l Ph.D. in Biotechnology of Resources and Environment, China Agricultural University (September 2008 - December 2011)
Supervisor: Professor Lu Yahai

l M.Sc. in Environmental Microbiology, Graduate School of the Chinese Academy of Agricultural Sciences (July 2004 - July 2007) Supervisor: Researcher Zhang Hui

l B.Sc. in Biotechnology, Anhui Normal University (September 2000 - July 2004)

 

Work Experience

l Researcher, Institute of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu (January 2018 - present)

l Associate Researcher, Institute of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu (January 2013 - December 2017)

l Assistant Researcher, Institute of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu (January 2010 - December 2012)

l Research Intern, Institute of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu (July 2007 - December 2009)

 

Research Work

    Dr. Cheng Lei specializes in the study of anaerobic microbial resources and their biotechnological applications. He has published over 40 papers in peer-reviewed journals and holds multiple invention patents. His primary research achievements include three publications in Nature: deciphering the fifth methanogenesis pathway for direct crude oil degradation to methane in single archaeon (Nature 2022), isolating the first methanogen outside the Euryarchaeota (Nature 2024), and identifying a new methanol-mediated syntrophic methanogenesis between bacteria and archaea (Nature 2025).

In addition, Dr. Cheng has proposed 20 new high-level taxonomic units, including new orders and families of anaerobic microorganisms. He also developed a long-term preservation and high-throughput screening platform and established the largest domestic repository of anaerobic microbial type strains, which currently conserves over 1,400 species.

 

Research Projects Led

1. National Natural Science Fund for Distinguished Young Scholars: Geological Microbiology (32325002), RMB 4 million, January 2024 - December 2028.

2. Chinese Academy of Agricultural Sciences "Innovative Leading Talent" Project, RMB 4 million, January 2024 - December 2028.

3. Supported by Sichuan Science and Technology Program: Research on the Mechanism of Artificially Synthesized Petroleum Hydrocarbons (Project No.: 2025ZYD0172), RMB 1,000,000, September 2025 – August 2028.Sichuan Provincial Natural Science Fund for Innovative Research Group on Anaerobic Microbial Resources and Utilization (Project No.: 2024NSFTD0020), RMB 600,000, January 2024 - December 2026.

4. National Natural Science Foundation of China "Water Cycle" Major Research Plan Integration Project: Targeted Isolation and Physiological and Ecological Functions of Important Uncultivable Microorganisms in the Water Cycle Carbon Cycle (92351301), RMB 3.2 million, January 2024 - December 2024.

5. National Natural Science Foundation of China "Water Cycle" Major Research Plan Cultivation Project: Carbon Metabolism Function of Verstraetearchaeota Archaea (92051108), RMB 810,000, January 2021 - December 2023.

6. Chinese Academy of Agricultural Sciences "Young Talent" Cultivation Project, RMB 2 million, November 2017 - October 2022.

7. National Natural Science Foundation of China General Program"Targeted Isolation of Syntrophaceae and Its Response Mechanism to High-Pressure Stress" (31570009), RMB 754,000, January 2016 - December 2019.

8. Sub-topic of National Science and Technology Major Project on "Large Oil and Gas Fields and Coalbed Methane Development": Mechanism and Technology of Coal Rock Biogasification (2016ZX05041001-003), RMB 1.8905 million, January 2016 - December 2019.

9. National Natural Science Foundation of China General Program "Targeted Isolation of Syntrophus sp. under Methanogenic Conditions and Its Hydrocarbon Degradation Gene Study" (31370060), RMB 150,000, January 2014 - December 2014.

10. Sub-topic of National "863" Project: Research on Microbial Enhanced Oil Recovery Technology in Medium and High-Temperature Oil Reservoirs (2013aa064401), RMB 930,000, January 2013 - December 2016.

11. Sinopec Research Project on "Key Technologies for Enhancing Metabolic Rate of Anaerobic Bacterial Consortia" (Contract No. P15072), RMB 2.8 million, January 2015 - December 2017.

12. Sichuan Provincial International Science and Technology Cooperation and Exchange Project: Anaerobic Bioremediation Technology for Petroleum Pollutants (2013HH0018), RMB 100,000, January 2013 - December 2014.

13. National Natural Science Fund for Young Scholars: Key Microbial Consortia in the Methanogenic Degradation of n-Hexadecane (30900049), RMB 200,000, January 2010 - December 2012.

 

Representative Academic Papers

1. Wu, K., Zhou, L., Li, J., Yang, M., Ma, S., Sousa, D.Z., Cheng, L.* (2026). Targeted isolation of H₂-dependent methylotrophic methanogens by a cocktail approach. Nature Protocols 21, 959-986

2. Wu, K.., Zhou, L., Li, J., Ma, S., Sousa, D.Z.*, Cheng, L.* (2026). Culturing the uncultured anaerobes from the perspective of microbial growth curves. Trends in Microbiology 34, 89-97

3. Huang Y, Igarashi K, Liu L, Mayumi D, Ujiie T, Fu L, Yang M, Lu Y, Cheng L*, Kato S*, Nobu MK*. Methanol transfer supports metabolic syntrophy between bacteria and archaea. Nature, 2025, 639: 190-195

4. Wu K, Zhou L, Tahon G, Liu L, Li J, Zhang J, Zheng F, Deng C, Han W, Bai L, Fu L, Dong X, Zhang C, Ettema TJG, Sousa DZ*, Cheng L*. Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature, 2024, 632(8027)

5. Yu T, Fu L, Wang Y, Dong Y, Chen Y, Wegener G, Cheng L*, Wang F*. Thermophilic Hadarchaeota grow on long-chain alkanes in syntrophy with methanogens. Nature Communications, 2024, 15(1): 6560.

6. Zhou Z, Zhang C-j, Liu P-f, Fu L, Laso-Pérez R, Yang L, Bai L-p, Li J, Yang M, Lin J-z, Wang W-d, Wegener G*, Li M*, Cheng L*. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature, 2022, 601: 257–262.

7. Cheng L*, Shi S-b, Yang L, Zhang Y, Dolfing J, Sun Y-g, Liu L-y, Li Q, Tu B, Dai L-r, Shi Q, Zhang H. Preferential degradation of long-chain alkyl substituted hydrocarbons in heavy oil under methanogenic conditions. Org. Geochem., 2019, 138: 103927.

 

Academic Papers Published in Recent Years

1. Wu, K., Zhou, L., Li, J., Yang, M., Ma, S., Sousa, D.Z., Cheng, L.* (2026). Targeted isolation of H₂-dependent methylotrophic methanogens by a cocktail approach. Nature Protocols 21, 959-986

2. Wu, K.., Zhou, L., Li, J., Ma, S., Sousa, D.Z.*, Cheng, L.* (2026). Culturing the uncultured anaerobes from the perspective of microbial growth curves. Trends in Microbiology 34, 89-97

3. Ding Hengwu, Zhou Zhuo, Cheng Lei. Advances in the Biogasification of Residual Crude Oil in Depleted Oil Reservoirs. Acta Microbiologica Sinica, 2025: 1-17.

4. Jiao J-Y, Ma S-C, Salam N, Zhou Z, Lian Z-H, Fu L, Chen Y, Peng C-H, OuYang Y-T, Fan H, Li L, Yi Y, Zhang J-Y, Wang J-Y, Liu L, Gao L, Oren A, Woyke T, Dodsworth JA, Hedlund BP, Li W-J, Cheng L. Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. Microbiome, 2024, 12(1): 123.

5. Peng C, Zhang X, Li J, Yang M, Ma S, Fan H, Dai L, Cheng L. Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov. Int. J. Syst. Evol. Microbiol., 2024, 74(3).

6. Wu K, Zhou L, Tahon G, Liu L, Li J, Zhang J, Zheng F, Deng C, Han W, Bai L, Fu L, Dong X, Zhang C, Ettema TJG, Sousa DZ, Cheng L. Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature, 2024.

7. Yu T, Fu L, Wang Y, Dong Y, Chen Y, Wegener G, Cheng L, Wang F. Thermophilic Hadarchaeota grow on long-chain alkanes in syntrophy with methanogens. Nature Communications, 2024, 15(1): 6560.

8. Zhang C-J, Zhou Z, Cha G, Li L, Fu L, Liu L-Y, Yang L, Wegener G, Cheng L, Li M. Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs. ISME J., 2024.

9. Fu L, Lai S, Zhou Z, Chen Z, Cheng L. Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China. Front. Microbiol., 2023, 14.

10. Yi Y, Dolfing J, Jin G, Fang X, Han W, Liu L, Tang Y, Cheng L. Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri. Water Res., 2023: 119664.

11. Yi Yue, Zhou Zhuo, Huang Yan, Cheng Lei. Advances and Prospects in Methanogenic Archaea Research in China. Acta Microbiologica Sinica, 2023, 63(05): 1796-1814.

12. Cha G, Liu Y, Yang Q, Bai L, Cheng L, Fan W. Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea. Appl. Environ. Microbiol., 2022, 0(0): e01574-01522.

13. Zhou Z, Zhang C-j, Liu P-f, Fu L, Laso-Pérez R, Yang L, Bai L-p, Li J, Yang M, Lin J-z, Wang W-d, Wegener G, Li M, Cheng L. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature, 2022, 601: 257–262.

14. Jiang F, Wang S, Zhang Y, Ma S, Huang Y, Fan H, Li Q, Wang H, Wang A, Liu H, Cheng L, Deng Y, Fan W. Variation of Metagenome From Feedstock to Digestate in Full-Scale Biogas Plants. Front. Microbiol., 2021, 12.

15. Jiao J-Y, Fu L, Hua Z-S, Liu L, Salam N, Liu P-F, Lv A-P, Wu G, Xian W-D, Zhu Q, Zhou E-M, Fang B-Z, Oren A, Hedlund BP, Jiang H-C, Knight R, Cheng L, Li W-J. Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria. ISME J., 2021, 15(10): 3005-3018.

16. Yang M, Li J, Lv X-m, Dai L-r, Wu K-j, Tu B, Lawson PA, Tang Y-q, Cheng L. Thermosynergistes pyruvativorans gen. nov., sp. nov., an anaerobic, pyruvate-degrading bacterium from Shengli oilfield, and proposal of Thermosynergistaceae fam. nov. in the phylum Synergistetes. Int. J. Syst. Evol. Microbiol., 2021, 71(9).

17. Cheng Lei, Ma Shichun, Wu Kejia, Zhang Hui, Deng Yu. Anaerobic Microbial Cultivation and Isolation: Past, Present, and Future. Acta Microbiologica Sinica, 2021, 61(04): 946-968.

18. Lv X-m, Yang M, Dai L-r, Tu B, Chang C, Huang Y, Deng Y, Lawson PA, Zhang H, Cheng L, Tang Y-q. Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes. Int. J. Syst. Evol. Microbiol., 2020, 70: 3361-3373.

19. Wu K, Dai L, Tu B, Zhang X, Zhang H, Deng Y, Lawson PA, Cheng L. Gudongella oleilytica gen. nov., sp. nov., an aerotorelant bacterium isolated from Shengli oilfield and validation of family Tissierellaceae. Int. J. Syst. Evol. Microbiol., 2020, 70: 951-957.

20. Lai Shouchao, Fang Xiaoyu, Tu Bo, Chen Hao, Deng Ze, Li Guizhong, Chen Zhenhong, Zhang Hui, Cheng Lei. Study on the Methanogenic Potential and Microbial Community Structure of Typical Coalbed Water. Acta Microbiologica Sinica, 2020, 60(4): 727–738.

21. Zhang Xue, Tu Bo, Liu Laiyan, Zeng Wanqiu, Cheng Lei. Characteristics of Short-Chain Fatty Acid Degradation by Syntrophic Hydrocarbon-Degrading Consortia. Journal of Applied and Environmental Biology, 2020, 26(3): 1-12.

22. Zhou Lei, Liu Laiyan, Liu Pengfei, Cheng Lei. Advances in Verstraetearchaeota Research. Bioresources, 2020, 42(05): 515-521.

23. Cheng L, Shi S-b, Yang L, Zhang Y, Dolfing J, Sun Y-g, Liu L-y, Li Q, Tu B, Dai L-r, Zhang H, Shi Q. Preferential degradation of long-chain alkyl substituted hydrocarbons in heavy oil under methanogenic conditions. Org. Geochem., 2019, 138: 103927.

24. Zhang X, Tu B, Lv X-m, Lawson PA, Yang M, Dai L-r, Zhang H, Tang Y-Q, Deng Y, Cheng L. Description of Biomaibacter acetigenes gen. nov., sp. nov., and proposal of Thermosediminibacterales ord. nov. containing two novel families of Tepidanaerobacteraceae fam. nov. and Thermosediminibacteraceae fam. nov. Int. J. Syst. Evol. Microbiol., 2019, 69(12): 3891-3902.

25. Zhang Xue, Zhang Hui, Cheng Lei. Isolation of Key Functional Consortia in Methanogenic Degradation of Organic Matter: Syntrophic Bacterial Cultures. Acta Microbiologica Sinica, 2019, 59(2): 211-223.

26. Zhang X, Tu B, Dai L-r, Lawson PA, Zheng Z-z, Liu L-Y, Deng Y, Zhang H, Cheng L. Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov. Int. J. Syst. Evol. Microbiol., 2018, 68: 3197-3211.

27. Ma T-T, Liu L-Y, Rui J-P, Yuan Q, Feng D-s, Zhou Z, Dai L-R, Zeng W-Q, Zhang H, Cheng L. Coexistence and competition of sulfate-reducing and methanogenic populations in an anaerobic hexadecane-degrading culture. Biotechnol. Biofuels, 2017, 10(1): 207.

28. Qin QS, Feng DS, Liu PF, He Q, Li X, Liu AM, Zhang H, Hu GQ, Cheng L. Metagenomic characterization of Candidatus Smithella cisternae strain m82_1, a syntrophic alkane-degrading bacteria, enriched from the shengli oil field. Microbes. Environ., 2017, 32(3): 234-243.

29. Cheng Lei, Zheng Zhenzhen, Wang Cong, Zhang Hui. Advances in Methanogenic Archaea Research. Microbiological Bulletin, 2016, 43(5): 1143-1164.

30. Wu Wei, Zheng Zhenzhen, Ma Tingting, Cheng Lei, Zhang Hui. Advances in Syntrophic Acetate Oxidizers. China Biogas, 2016, 34(2): 3-8.

31. Ma Tingting, Cheng Lei, Liu Laiyan, Dai Lirong, Zhou Zheng, Zhang Hui. Effects of Different Inhibitors on Methanogenic Acetate Degradation and Methanogenic Community Structure. Acta Microbiologica Sinica, 2015, 55(5): 587-597.

32. Ding Chen, Ma Ting, Hu An, Dai Li, He Qiao, Cheng Lei, Zhang Hui. Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions. Microbial Ecology, 2015, 70(2): 433-444.

33. Cheng L, Shi S, Li Q, Chen J, Zhang H, Lu Y. Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions. PLoS One, 2014, 9(11): e113253.

34. Ding Chen, Cheng Lei, He Qiao, Zhang Hui. Characteristics of Fatty Acid Degradation by Syntrophic Hydrocarbon-Degrading Consortia M82. Acta Microbiologica Sinica, 2014, 54(11): 1369-1377.

35. Ma Tingting, Cheng Lei, Zheng Zhenzhen, Qin Qianshan, Zhang Hui. Comparison of DNA Extraction Methods for Petroleum Hydrocarbon-Degrading Methanogenic Consortia. China Biogas, 2014, 32(3): 3-7.

36. Ma Tingting, Cheng Lei, Zheng Zhenzhen, Qin Qianshan, Dai Lirong, Zhang Hui. Effects of Different pH Buffers on Methanogenic Community Structure from Acetate. Acta Microbiologica Sinica, 2014, 54(12): 1453-1461.

37. Cheng L, Rui J, Li Q, Zhang H, Lu Y. Enrichment and dynamics of novel syntrophs in a methanogenic hexadecane-degrading culture from a Chinese oilfield. FEMS Microbiol. Ecol., 2013, 83(3): 756-766.

38. Cheng L, He Q, Ding C, Dai L-r, Li Q, Zhang H. Novel bacterial groups dominate in a thermophilic methanogenic hexadecane-degrading consortium. FEMS Microbiol. Ecol., 2013, 85(3): 568-577.

39. Cheng L, Ding C, Li Q, He Q, Dai LR, Zhang H. DNA-SIP reveals that Syntrophaceae play an important role in methanogenic hexadecane degradation. PLOS ONE, 2013, 8(7): e66784.

40. He Qiao, Ding Chen, Li Guizhong, Chen Hao, Cheng Lei, Zhang Hui. Study on the Biochemical Methane Potential of Coal with Different Maturities. Acta Microbiologica Sinica, 2013, 54(12): 1307-1317.

41. Zhang Yu, Zhang Hui, Guo Shengxue. Petroleum Microbiology (Translation). Beijing: China石化Press, 2011.

42. Cheng L, Dai L, Li X, Zhang H, Lu Y. Isolation and characterization of Methanothermobacter crinale sp. nov, a novel hydrogenotrophic methanogen from Shengli Oilfields. Appl. Environ. Microbiol., 2011, 77(15): 5212-5219.

43. Feng Y, Cheng L, Zhang X, Li X, Deng Y, Zhang H. Thermococcoides shengliensis gen. nov., sp. nov., a new member of the order Thermotogales isolated from oil-production fluid. Int. J. Syst. Evol. Microbiol., 2010, 60(4): 932-937.

44. Cheng L, Qiu T-l, Li X, Wang W-d, Yin X, Deng Y, Zhang H. Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, P. R. China. FEMS Microbiol. Lett., 2008, 285: 65-71.

45. Li Xia, Cheng Lei, Wang Weidong, Deng Yu, Yin Xiaobo, Zhang Hui. Isolation, Identification and Metabolic Characteristics of a Thermophilic Anaerobic Bacillus from Oil Reservoir. Acta Microbiologica Sinica, 2008, 48(8): 995-1000.

46. Li Xia, Cheng Lei, Deng Yu, Zhang Hui. Advances in Anaerobic Biodegradation of Petroleum Hydrocarbons. Journal of Applied and Environmental Biology, 2008, 14(2): 283-289.

47. Cheng L, Qiu T-L, Yin X-B, Wu X-L, Hu G-Q, Deng Y, Zhang H. Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Int. J. Syst. Evol. Microbiol., 2007, 57(12): 2964-2969.

48. Qiu Tianlei, Cheng Lei, Luo Hui, Zhang Hui, Wu Xiaolei, Deng Yu. Isolation and Identification of a Methanogenic Archaeon from Offshore Sediments. China Biogas, 2007, 25(02): 3-6.

49. Cheng Lei, Qiu Tianlei, Deng Yu, Zhang Hui. Advances in Methanogenic Archaea Research in China. 50th Anniversary Paper Collection of the Chinese Academy of Agricultural Sciences, 2007: 355-363.

50. Cheng Lei, Qiu Tianlei, Deng Yu, Zhang Hui. Advances in Anaerobic Microbial Research in Oil Reservoirs. Journal of Applied and Environmental Biology, 2006, 12(5): 740-744.