Research Interests

 ・ Dissecting natural microbial community dynamics and biogeochemical cycles

 ・ Investigating microbial and ecosystem responses to our changing environment

 ・ Exploring and utilizing the extreme microbial genetic and function potentials

Research Projects

 ・ Biological oxidation of methane

 ・ Microbial metal metabolism

 ・ Microbial interactions and symbiosis

Admission and Job Opportunities

Looking for motivated masters/PhD students and postdocs in any relevant research field (microbiology, environmental science, bioengineering, chemical engineering, ecology etc).

Please email me your CV along with a brief paragraph describing your research and career interests.

2011.09-2017.06, M.Sc. and Ph.D., Environmental Science and Engineering, California Institute of Technology (Advisor: Victoria J. Orphan)

2006.09-2010.05, B.Sc., Honors in Microbiology and Immunology, University of British Columbia (Advisor: William W. Mohn)

2022.12-, Assistant Professor, Department of Physical Geography and Natural Resources, College of Urban and Environmental Sciences, Peking University

2020.07-2022.06, Postdoc, University of Southern California (Advisor: Moh Y. El-Naggar)

2017.08-2020.02, Postdoc, California Institute of Technology (Advisors: Victoria J. Orphan and Jared R. Leadbetter)

2010.06-2010.12, Research Assistant, Monterey Bay Aquarium Research Institute (Advisors: Sebastian Sudek and Alexandra Z. Worden)

2009.01-2009.10, Team Member, UBC International Genetically Engineered Machines iGEM Inangural Team (Gold Medal)

Environmental Microbiology, Microbial Ecology, Geomicrobiology

Full publication list: https://scholar.google.com/citations?hl=en&user=3no8Uy8AAAAJ

(*=corresponding authors)

Yu, H.*, Xu, S., Jangir, Y., Wegener, G., Orphan, V.J.*, and El-Naggar, M.Y.* (2025) Redox conduction facilitates direct interspecies electron transport in anaerobic methanotrophic consortia. Science Advances. eadw4289. https://doi.org/10.1126/sciadv.adw4289

Lyu, X., Yu, H.*, and Lu, Y.* (2025) Diversity and function of soluble heterodisulfide reductases in methane-metabolizing archaea. Microbiology Spectrum. 13(5) e03238-24. https://doi.org/10.1128/spectrum.03238-24

Rodríguez, O., Metcalfe, K.S., McGlynn, S.E., Yu, H., Dekas, A.E., Ellisman, M., Deerinck, T., Grotzinger, J.P., and Orphan, V.J. (2023) Microbially-induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation. Proceedings of the National Academy of Sciences, 120 (51) e2302156120. https://doi.org/10.1073/pnas.2302156120

Murali, R., Yu, H., Speth, D.R., Wu, F., Metcalfe, K. S., Crémière, A., Laso-Pèrez, R., Malmstrom, R.R., Goudeau, D., Woyke, T., Hatzenpichler, R., Chadwick, G.L., Connon, S.A., and Orphan, V.J. (2023). Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea. PLoS Biology, 21(9), e3002292. https://doi.org/10.1371/journal.pbio.3002292

Yu, H.*, Speth, D.R., Connon, S.A., Goudeau, D., Malmstrom, R.R., Woyke, T., and Orphan, V.J.* (2022) Community structure and microbial associations in sediment-free methanotrophic enrichment cultures from a marine methane seep. Applied and Environmental Microbiology. e02109-21. https://doi.org/10.1128/aem.02109-21

Heryakusuma, C., Susanti, D., Yu, H., Li, Z., Purwantini, E., Hettich, R.L., Orphan, V.J., and Mukhopadhyay, B. (2022) A reduced F420-dependent nitrite reductase (FNiR) in an anaerobic methanotrophic archaeon. Journal of Bacteriology. e00078-22. https://doi.org/10.1128/jb.00078-22

Yu, H.*, Chadwick, G.L., Lingappa, U.F., and Leadbetter J.R.* (2022) Comparative genomics on cultivated and uncultivated, freshwater and marine “Candidatus Manganitrophaceae” species implies their worldwide reach in manganese chemolithoautotrophy. mBio. 13 (2), e03421-21. https://doi.org/10.1128/mbio.03421-21

Chadwick, G. L., Skennerton, C. T., Laso-Pérez, R., Leu, A. O., Speth, D. R., Yu, H., Morgan-Lang, C., Hatzenpichler, R., Goudeau, D., & Malmstrom, R. (2022). Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biology 20 (1): e3001508. https://doi.org/10.1371/journal.pbio.3001508

Yu, H., Skennerton, C.T., Chadwick, G.L., Leu, A.O., Aoki, M., Tyson, G.W., and Orphan V.J. (2022) Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea. The ISME Journal 16, 168–177. https://doi.org/10.1038/s41396-021-01047-0 (Editors’ Choice)

Yu, H., Leadbetter, J.R. (2020) Bacterial chemolithoautotrophy via manganese oxidation. Nature 583, 453–458. https://doi.org/10.1038/s41586-020-2468-5 (Nature Cover)

Yu, H., Susanti, D., McGlynn, S.E., Skennerton, C.T., Chourey, K., Iyer, R., Scheller, S., Tavormina, P., Hettich, R.L., Mukhopadhyay, B., and Orphan, V.J. (2018) Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea. Frontiers in Microbiology. 9. https://doi.org/10.3389/fmicb.2018.02917

Scheller, S., Yu, H., Chadwick, G.L., McGlynn, S.E., and Orphan, V.J. (2016) Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction. Science 351: 703–707. https://doi.org/10.1126/science.aad7154 (Science Perspective)

van Baren, M.J., Bachy, C., Reistetter, E.N., Purvine, S.O., Grimwood, J., Sudek, S., Yu, H., Poirier, C., Deerinck, T.J., Kuo, A., Grigoriev, I.V., Wong, C., Smith, R.D., Callister, S.J., Wei, C., Schmutz, J., and Worden, A.Z. (2016) Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics 17: 267. https://doi.org/10.1186/s12864-016-2585-6

Glass, J.B., Yu, H., Steele, J.A., Dawson, K.S., Sun, S., Chourey, K., Pan, C., Hettich, R.L., Orphan, V.J. (2014) Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments. Environmental Microbiology 6, 1592-1611. https://doi.org/10.1111/1462-2920.12314

Hartmann, M., Howes, C.G., VanInsberghe, D., Yu, H., Bachar, D., Christen, R., Nilsson, R.H., Hallam, S.J. and Mohn, W.W. (2012) Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. The ISME Journal 6, 2199–2218. https://doi.org/10.1038/ismej.2012.84

Patents

Scheller, S., Orphan, V. J. and Yu, H. (2017). Methane oxidation methods and compositions. United States Patent No. US20170107479A1.

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