Research Interests
Microbial Physiology and Ecology, Environmental Microbiology, Biological Oceanography, Archaeal Biology, Microbial Nitrogen Cycle, Biogeochemistry
Research Description
My research interests focus on gaining a better understanding of the biogeochemical role of globally significant microorganisms that shape marine and terrestrial nutrient transformations, the ecological principles and environmental controls that govern their distribution, activity, and interaction in natural and engineered ecosystems, and the molecular and metabolic mechanisms that underpin their adaptations and stress responses to anthropogenic perturbations and global climate change processes.
I apply physiological methods, Next-Generation Sequencing approaches, MS-based proteomics and metabolomics techniques, microbial genetics, and bioinformatics tools to comprehensively evaluate the activity, regulation, and interaction of microorganisms in complex environments. My current model microorganisms are nitrifying microorganisms (i.e. nitrifiers), including Ammonia-oxidizing Archaea (AOA), Ammonia-oxidizing Bacteria (AOB), Complete Ammonia oxidizer (Comammox), and Nitrite-oxidizing Bacteria (NOB), which collectively drive the oxidation of reduced forms of nitrogen to nitrate and provide essential links in the nitrogen cycle of natural and engineered systems. Nitrifiers are one of the most abundant and ubiquitous organisms in the global biosphere, and they make a significant contribution to global carbon fixation through chemosynthetic pathways, the production of potent greenhouse gas nitrous oxide, and the provision of the often-limiting cofactor cobalamin (vitamin B12) in marine and terrestrial ecosystems.
My lab aims to combine culture-based lab work and meta-omics-based field study to characterize the novel physiological and metabolic adaptive features that support the ecological success of these globally abundant nitrifiers, the metabolic and signaling interaction between nitrifiers and other associated biota, and the impact of anthropogenic perturbation and global changes on nitrifying microbial community dynamics and nutrient cycling in various ecosystems.
Education
B.S., Environmental Science, Beijing Normal University, 2010
Ph.D., Environmental Microbiology, University of Washington, 2016
Simons Foundation Postdoctoral Fellow, University of Washington, 2017-2020
Awards and Honors
Simons Foundation Early Career Award in Aquatic Microbial Ecology and Evolution, 2025
Department of Energy Early Career Award, 2024
Nancy L. Mergler Faculty Mentor Award for Undergraduate Research, 2023
Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology, 2017
Additional Campus Affiliations
External Links
Highlighted Publications
Qin, W.*#, Wei, S.P.#, Zheng, Y. #, Choi, E.#, Li, X., Johnston, J., Wan, X., Abrahamson, B., Flinkstrom, Z., Wang, B., Li, H., Hou, L., Tao, Q., Chlouber, W.W., Sun, X., Wells, M., Ngo, L., Hunt, K.A., Urakawa, H., Tao, X., Wang, D., Yan, X., Wang, D., Pan, C., Weber, P.K., Jiang, J., Zhou, J., Zhang, Y., Stahl, D.A., Ward, B.B., Mayali, X., Martens-Habbena, W.*, Winkler, M.H*. (2024) Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature Microbiology (*Corresponding author) https://doi.org/10.1038/s41564-023-01593-7
Zheng, Y., Wang, B., Gao, P., Yang, Y., Su, X., Ning, D., Zhao, F., Wang, D., Zhang, Y., Li, M., Winkler, M.K.H., Ingalls, A.E., Zhou, J., Zhang, C., Stahl, D.A., Jiang, J.*, Martens-Habbena, W.*, Qin, W.*. (2024) Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. ISME Journal (*Corresponding author) https://doi.org/10.1093/ismejo/wrad002
Wan, S., Hou, L., Kao, S., Zhang, Y., Sheng, H., Shen, H., Tong, S., Qin, W., Ward, B.B. (2023) Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling. PNAS 120: e2220697120. https://www.pnas.org/doi/abs/10.1073/pnas.2220697120
Martens-Habbena, W., Qin, W. (2022). Archaeal nitrification without oxygen. Science 375: 27-28. https://DOI.org/10.1126/science.abn0373
Qin, W.*, Zheng, Y., Wang, Y., Urakawa, H., Martens-Habbena, W., Liu, H., Huang, X., Zhang, X., Nakagawa, T., Mende, D.R., Bollmann, A., Wang, B., Zhang, Y., Amin, S.A., Nielsen, J.L., Mori, K., Takahashi, R., Armbrust., E.V., Winkler, M.H., DeLong, E.F., Li, M., Lee, P., Zhou, J., Zhang, C., Zhang, T., Stahl, D.A., Ingalls, A.E. (2020) Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME Journal. *Corresponding author https://doi.org/10.1038/s41396-020-0710-7
Zhang, Y., Qin, W., Hou, L., Zakem, E.J., Wan, X., Zhao, Z., Liu, L., Hunt, K., Jiao, N., Kao, S., Tang, K., Xie, X., Shen, J., Li, Y., Chen, M., Dai, X., Liu, C., Deng, W., Dai, M., Ingalls, A.E., Stahl, D.A., Herndl, G.J. (2020) Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. PNAS. https://doi.org/10.1073/pnas.1912367117
Wang, B.†, Qin, W.†, Ren, Y†, Zhou, X., Jung, M.Y., Han, P., Eloe-Fadrosh, E.A., Li, M., Zheng, Y., Lu, L., Yan, X., Ji, J., Liu, Y., Liu, L., Heiner, C., Hall, R., Martens-Habbena, W., Herbold, C.W., Rhee, S., Bartlett, D.H., Huang, L., Ingall, A.E., Wagner, M., Stahl, D.A., Jia, Z. (2019) Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME Journal. †Joint first author https://doi.org/10.1038/s41396-019-0493-x
Qin, W., Amin, S.A., Lundeen, R.A., Heal, K.R., Martens-Habbena, W., Turkarslan, S., Urakawa, H., Coata, K.C., Hendrickson, E.L., Wang, T., Beck, D.AC., Tiquia-Arashiro, S.M., Taub, F., Holmes, A.D., Vajrala, N., Berube, P.M., Lowe, T.M., Moffett, J.W., Devol, A.H., Baliga, N.S., Arp, D.J., Sayavedra-Soto, L.A., Hackett, M., Armbrust, E.V., Ingalls, A.E., Stahl, D.A. (2018) Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. ISME Journal. https://doi.org/10.1038/ismej.2017.186
Horak, R.E.A., Qin, W., Bertagnolli, A.D., Nelson, A., Heal, K.R., Han, H., Heller, M., Schauer, A., Jeffrey. W.H., Armbrust, E.V., Moffett, J.W., Ingalls, A.E., Stahl, D.A., Devol, A.H. (2017) Relative impacts of light, temperature, and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean. Limnology and Oceanography. https://doi.org/10.1002/lno.10665
Heal, K.R., Qin, W., Ribalet, F., Bertagnolli, A.D., Coyote-Maestas, W., Hmelo, L.R., Moffett, J.W., Devol, A.H., Armbrust, E.V., Stahl, D.A., Ingalls, A.E. (2017) Two distinct pools of B12 analogs reveal community interdependencies in the ocean. PNAS 114: 364-369. https://doi.org/10.1073/pnas.1608462114
Qin, W., Carlson, L.T., Armbrust, E.V., Devol, A.H., Moffett, J.W., Stahl, D.A., and Ingalls, A.E. (2015) Confounding effects of oxygen and temperature on the TEX86 signature of marine Thaumarchaeota. PNAS 112: 10979-10984. https://doi.org/10.1073/pnas.1501568112
Qin, W., Amin, S.A., Martens-Habbena, W., Walker, C.B., Urakawa, H., Devol, A.H., Ingalls, A.E., Moffett, J.W., Armbrust, E.V., Stahl, D.A. (2014) Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. PNAS 111: 12504-12509. https://doi.org/10.1073/pnas.1324115111
Recent Publications
Su, Y., Guo, X., Gao, Y., Feng, J., Wu, L., Lei, J., Liu, S., Gao, Q., Zeng, Y., Qin, W., Shi, Z., Liang, Z., Ye, Z., Yuan, M., Ning, D., Wu, L., Zhou, J., Yang, Y. (2025) Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms. ISME Communications. https://doi.org/10.1093/ismeco/ycae152
Myllykallio, H., Qin, W., Berg, I.A. (2025) The metabolic pathways of Archaea. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1648560
Tao, X., Yang, Z., Feng, J., Jian, S., Yang, Y., Bates, C.T., Wang, G., Guo, X., Ning, D., Kempher, M.L., Liu, X., Ouyang, Y., Han, S., Wu, L., Zeng, Y., Kuang, J., Zhang, Y., Zhou, X., Shi, Z., Qin, W., Wang, J., Firestone, M.K., Tiedje, J.M., Zhou, J. (2024) Climate warming accelerates positive soil priming in a temperate grassland ecosystem. Nature Communications. https://doi.org/10.1038/s41467-024-45277-0
Zhao, Z., Qin, W., Li, L., Zhao, H., Ju, F. (2024) Discovery of Candidatus Nitrosomaritimum as a new genus of ammonia-oxidizing archaea widespread in anoxic saltmarsh intertidal aquifers. Environmental Science & Technology. https://doi.org/10.1021/acs.est.4c02321
Liu, L., Chen, M., Wan, X., Du, C., Liu, Z., Hu, Z., Jiang, Z., Zhou, K., Lin, H., Shen, H., Zhao, D., Y, L., Hou, L., Yang, J., Li, X., Kao, S., Zakem, E.J., Qin, W., Dai, M., Zhang, Y. (2023) Reduced nitrite accumulation at the primary nitrite maximum in the cyclonic eddies in the western North Pacific subtropical gyre. Science Advances. DOI: 10.1126/sciadv.ade2078
