2024
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
2023
Zhang, L., Chen, M., Zheng, Y., Wang, J., Xiao, X., Chen, X., Hu, C., Shen, J., Liu, J., Tang, K., Zhang, R., Xu, D., Shi, Q., Ning, X., Thomas, H., Qin, W., Zhao, M., Jiao, N., Zhang, Y. (2023) Microbially driven fate of terrigenous particulate organic matter in oceans. Limnology & Oceanography https://doi.org/10.1002/lno.12255
Zhou, J., Song, W., Qin, W., Liu, J., Stahl, D.A., Jiao, N., et al. (2023) The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean. mLife https://doi.org/10.1002/mlf2.12095
Li, T., Li, P., Qin, W., Wu, Meng, Saleem, M., Kuang, L., et al. (2023) Fertilization weakens the ecological succession of dissolved organic matter in paddy rice rhizosphere soil at the molecular level. Environmental Science & Technology https://doi.org/10.1021/acs.est.3c05939
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, 9,eade2078. DOI:10.1126/sciadv.ade2078
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
2022
Gottshall, E.Y., Godfrey, B., Li, B., Abrahamson, B., Qin, W., Winkler, M. (2022) Photoinhibition of comammox reaction in Nitrospira inopinata in a dose- and wavelength-dependent manner. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2022.1022899
Nie, Z., Xu, X., Shao, N., He, J., Li, P., Xu, P., Hu, J., Qin, W., Wang, B., Xu, G. (2022) Integrative analysis of microbiome and metabolome reveals the linkage between gut microbiota and carp growth. Environmental Research https://doi.org/10.1016/j.envres.2022.115133
Zakem, E., Bayer, B., Qin, W., Santoro, A., Zhang, Y., Levine, N.M. (2022) Controls on the relative abundances and rates of nitrifying microorganisms in the ocean. Biogeosciences. https://doi.org/10.5194/bg-2022-139
Zhang, L., Chen, M., Zheng, Y., Wang, J., Xiao, X., Chen, X., Hu, C., Shen, J., Liu, J., Tang, K., Zhang, R., Xu, D., Shi, Q., Ning, X., Thomas, H., Qin, W., Zhao, M., Jiao, N., Zhang, Y. (2022) Microbially driven fate of terrigenous particulate organic matter in oceans. Limnology & Oceanography. https://doi.org/10.1002/lno.12255
He, Z., Lin, L., Wang, X., Qin, W., Zhang, C. (2022) Editorial: Carbon Storage by Marine Microorganisms for Carbon Neutrality. Frontiers in Marine Science. https://doi.org/10.3389/fmars.2022.1018397
Wang, H., Zheng, Y., Liu, J., Zhu, B., Qin, W., Zhao, F. (2022) An electrochemical system for the rapid and accurate quantitation of microbial exoelectrogenic ability. Biosensors and Bioelectronics. 215, 114584. https://doi.org/10.1016/j.bios.2022.114584
Durham, B.P., Boysen, A.K., Heal, K.R., Carlson, L.T., Boccamazzo, R., Deodato, C.R., Qin, W., Cattolico, R.A., Armbrust, E.V., Ingalls, A.E. (2022) Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton. Frontiers in Marine Science. https://doi.org/10.3389/fmars.2022.864796
Zhang, S., Xia, X., Wang, J., Li, X., Xin, Y., Bao, J., Han, L., Qin, W., Yang, Z. (2022) Biogeographic patterns and elevational differentiation of sedimentary bacterial communities across river systems in China. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.00597-22
Song, W., Liu, J., Qin, W., Huang, J., Yu, X., Xu, M., Stahl, D.A., Jiao, N., Zhou, J., Tu, Q. (2022) Functional traits resolve mechanisms governing the assembly and distribution of nitrogen-cycling microbial communities in the global ocean. mBio. https://doi.org/10.1128/mbio.03832-21
Martens-Habbena, W., Qin, W. (2022). Archaeal nitrification without oxygen. Science. 375: 27-28. https://DOI.org/10.1126/science.abn0373
2021
Kong, L., He, Y., Xie, Z., Luo, X., Zhang, H., Yi, S., Lin, Z., Zhang, S., Yan, K., Xu, H., Jin, T., Lin, L., Qin, W., Chen, F., Liu, S., Wang, D. (2021) Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean’s twilight zone by metaproteomics. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.00986-21
Zhou, J., Yu, X., Liu, J., Qin, W., He, Z., Stahl, D.A., Jiao, N., Zhou, J., and Tu, Q. (2021) VB12Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways. mSystems. https://doi.org/10.1128/mSystems.00497-21
Heal, K.R., Durham, B.P., Boysen, A.K., Carlson, L.T., Qin, W., Ribalet, F., White, A.E., Bundy, R.M., Armbrust, E.V., Ingalls, A.E. (2021) Marine community metabolomes carry fingerprints of phytoplankton community composition. mSystems. https://doi.org/10.1128/mSystems.01334-20
Wang, Y., Qin, W., Jiang, X., Ju, F., Mao, Y., Zhang, A., Stahl, D.A., Zhang, T. (2021) Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis. Environmental Science & Technology. https://doi.org/10.1021/acs.est.0c07703
2020
Yang, Y., Herbold, C.W., Jung, MY., Qin, W., Cai, M., Du, H., Lin, JG., Li, X., Li, M., Gu, JD. (2020) Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration. Water Research. https://doi.org/10.1016/j.watres.2020.116798
Stein, L.Y., Klotz, M.G., Lancaster, K.M., Nicol, G.W., Qin, W., Schleper, C., Stahl, D.A., Ward, B.B., Yoon, S. (2020) Comment on“A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea” by Lan Wu, Xueming Chen, Wei Wei, Yiwen Liu, Dongbo Wang, and Bing-Jie Ni. Environmental Science & Technology. https://doi.org/10.1021/acs.est.0c06792
Zhang S., Qin W., Bai Y., Zhang Z., Wang J., Gao H., Gu JD., Xia X. (2020) Linkages between anammox and denitrifying bacterial communities and nitrogen loss rates in high‐elevation rivers. Limnology and Oceanography. https://doi.org/10.1002/lno.11641
Chen, S., Xu H., Qin W., Xu S., Tang X., Kuang L., Wang X., Jiang B., Chen J., Shan J., Adams J., Qin H., Wang, B. (2020) Evaluation of Two Primer Sets for Amplification of Comammox Nitrospira amoA Genes in Wetland Soils. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2020.560942
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
Zheng, Y., Wang, H., Liu, Y., Zhu, B., Li, J., Yang, Y., Qin, W., Chen, L., Wu, X., Chistoserdova, L., Zhao, F. (2020) Methane-Dependent Mineral Reduction by Aerobic Methanotrophs under Hypoxia. Environmental Science & Technology Letters. https://doi-org.offcampus.lib.washington.edu/10.1021/acs.estlett.0c00436
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
Zhang S., Qin, W., Xia X., Li, S., Xia L., Zhang L., and Bai Y. (2020) Ammonia oxidizers in rivers of the Qinghai-Tibetan Plateau and their adaptations to high-elevation conditions. Water Research. https://doi.org/10.1016/j.watres.2020.115589
2019
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
2018
Heal, K.R., Qin, Wei., Amin, S.A., Devol, A.H., Moffett, J.W., Armbrust, E.V., Stahl, D.A., Ingalls, A.E. (2018) Accumulation of NO2‐cobalamin in nutrient‐stressed ammonia‐oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific. Environmental Microbiology Reports. https://doi.org/10.1111/1758-2229.12664
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
2017
Qin, W., Heal, K.R., Ramdasi, R., Kobelt, J.N., Martens-Habbena, W., Bertagnolli, A.D., Amin, S.A., Walker, C.B., Urakawa, H., Könneke, M., Devol, A.H., Moffett, J.W., Armbrust, E.V., Jensen, G.J., Ingalls, A.E., Stahl, D.A. (2017) Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology. https://doi.org/10.1099/ijsem.0.002416
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
Qin, W., Meinhardt, K.A., Moffett, J.W., Devol, A.H., Armbrust, E.V., Ingalls, A.E., and Stahl, D.A. (2017) Influence of oxygen availability on the activities of ammonia-oxidizing archaea. Environmental Microbiology Reports. https://doi-org.offcampus.lib.washington.edu/10.1111/1758-2229.12525
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., Jewell, T.N.M., Russell, V.V., Hedlund, B.P., de la Torre, J.R., Stahl, D.A. (2017) Candidatus Nitrosocaldus. Bergey’s Manual of Systematics of Archaea and Bacteria. https://doi.org/10.1002/9781118960608.gbm01287
2016
Qin, W., Martens-Habbena, W., Kobelt, J.N., Stahl, D.A. (2016) Candidatus Nitrosopumilus. Bergey’s Manual of Systematics of Archaea and Bacteria. https://onlinelibrary.wiley.com/doi/abs/10.1002/9781118960608.gbm01290
2015
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
Martens-Habbena, W.†, Qin, W.†, Horak, R.E.A., Urakawa, H., Schauer, A.J., Moffett, J.W. Armbrust, E.V., Ingalls, A.E., Devol, A.H., Stahl, D.A. (2015) The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger. Environmental Microbiology. 17: 2261-2274. †Joint first author https://doi.org/10.1111/1462-2920.12677
2014
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
2013
Horak, R.E.A., Qin, W., Schauer, A.J., Armbrust, E.V., Ingalls, A.E., Moffett, J.W., Stahl, D.A., Devol, A.H. (2013) Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea. ISME Journal 7: 2023-2033. https://doi.org/10.1038/ismej.2013.75
