通过跨学科的方法，在冷泉深部生物圈方面取得了如下重要发现：（1）揭示了深海冷泉微生物及其病毒的系统发育多样性、生物地理分布模式、代谢能力和进化轨迹；（2）阐明了厌氧烃降解与冷泉中其他生物地球化学过程（包括金属循环、生物固氮、氢代谢和还原脱卤作用）之间的相互作用；（3）发现了冷泉中大量以前未开发的遗传资源，包括编码抗菌化合物的多样生物合成基因簇、多种抗病毒系统家族以及汞还原酶等资源。
9) Han, Y.; Liao, J.; Li, C.; Xing, F.; Peng, J.; Liu, X.; Xie, W.; Wu, F.; Jian, H.; Cheng, R.; Dong, X., Diverse defense systems synergistically drive the microbe-virus arms race in deep sea cold seeps. Preprint at bioRxiv 2024, 2024.09.26.614923.
8) Zhang, C.; He, Y.; Wang, J.; Chen, T.; Baltar, F.; Hu, M.; Liao, J.; Xiao, X.; Li, Z.-R.; Dong, X., Illuminating microbial phosphorus cycling in deep-sea cold seep sediments using protein language models. Preprint at bioRxiv 2024, 2024.07.09.602434.
7) Wu, L.; Liu, Y.; Shi, W.; Chang, T.; Liu, P.; Liu, K.; He, Y.; Li, Z.; Shi, M.; Jiao, N.; Dong, X.; Zheng, Q., Alpine lakes harbor diverse, endemic and structurally unique RNA viruses. Preprint at bioRxiv 2024, 2024.07.04.601995.
6) Jiang Q; Cao, L; Han Y.; Li, S.; Zhao, R.; Zhang X.; Ruff, S.E.; Zhao Z.; Peng J.; Liao J.; Zhu B.; Wang M.; Lin X.; Dong X., Cold seeps are hotspots of deep-sea nitrogen-loss driven by microorganisms across 21 phyla. Preprint at bioRxiv 2024.06.05.597523; doi: https://doi.org/10.1101/2024.06.05.597523.
5) Han, Y., Peng, Y., Peng, J., Cao, L., Xu, Y., Yang, Y., Wu, M., Zhou, H., Zhang, C., Zhang, D., Wang, M., Greening C., Dong, X. 2024. Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps. Preprint at bioRxiv, 2024.01. 23.576788.
4) Leung, P. M.; Jeffrey, L. C.; Bay, S. K.; Gomez-Alvarez, P.; Hall, M.; Johnston, S. G.; Dittmann, J.; Jirapanjawat, T.; Hutchinson, T. F.; Coleman, N. V.; Dong, X.; Deschaseaux, E.; Maher, D. T.; Greening, C., Wetland tree barks are dynamic hotspots for microbial trace gas cycling. Preprint at bioRxiv 2024, 2024.07.02.601631.
3) Zhang, T.; Han, Y.; Peng, Y.; Deng, Z.; Shi, W.; Xu, X.; Wu, Y.; Dong, X., Microbial virulome and resistome in deep-sea cold seeps pose minimal public health risks. Preprint at bioRxiv 2024, 2024.11.25.625267.
2) Peng, J.; Liu, X.; Wang, J.; Meng, N.; Cai, R.; Peng, Y.; Han, Y.; Liao, J.; Li, C.; Rubin-Blum, M.; Ma, Q.; Dong, X., Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps. Preprint at bioRxiv 2024, 2024.11.15.623595.
1) Liang, Q.; Liu, X.; Wang, J.; Chen, T.; Han, Y.; Zhang, L.; Li, S.; Zhao, J.; Dong, Y.; Guo, B.; Xiao, X.; Dong, X., Microbial succession, community assembly and adaptation over five years in a newly discovered deep-sea cold seep. Preprint at bioRxiv 2024, 2024.10.31.619006.
Peer Reviewed Articles:
51) Li, C.; Zhang, Y.; Shi, W.; Peng, Y.; Han, Y.; Jiang, S.; Dong, X.; Zhang, R., Viral diversity within marine biofilms and interactions with corrosive microbes. Environmental Research 2024, 263, 119991.
50) Han, P.; Tang, X.; Koch, H.; Dong, X.; Hou, L.; Wang, D.; Zhao, Q.; Li, Z.; Liu, M.; Lücker, S.; Shi, G., Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica. Nature Communications 2024, 15, (1), 3143.
49) Li, Q.; Ma, Z.; Huo, J.; Zhang, X.; Wang, R.; Zhang, S.; Jiao, J.; Dong, X.; Janssen, P. H.; Ungerfeld, E. M.; Greening, C.; Tan, Z.; Wang, M., Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield. The ISME Journal 2024, 18, (1), wrad016
48) Xu, Y.; Teng, Y.; Dai, S.; Liao, J.; Wang, X.; Hu, W.; Guo, Z.; Pan, X.; Dong, X.; Luo, Y., Atmospheric Trace Gas Oxidizers Contribute to Soil Carbon Fixation Driven by Key Soil Conditions in Terrestrial Ecosystems. Environmental Science & Technology 2024, 58, (49), 21617-21628.
47) Wang, S.; Jiang, L.; Zhao, Z.; Chen, Z.; Wang, J.; Alain, K.; Cui, L.; Zhong, Y.; Peng, Y.; Lai, Q.; Dong, X.; Shao, Z., Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments. ISME J 2024, 18, (1).
46) Li, J.; Dong, X.; Tang, Y.; Zhang, C.; Yang, Y.; Zhang, W.; Liu, S.; Feng, X.; Shang, L.; Peng, X., Deep sea cold seeps are a sink for mercury and source for methylmercury. Communications Earth & Environment 2024, 5 (1), 324..
45) Chen, Y., Dong, X., Sun, Z., Xu, C., Zhang, X., Qin, S., Geng, W., Cao, H., Zhai, B., Li, X., Wu, N. 2024. Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments. Microbiol Spectr, e0349023.
44) Dong, X., Zhang, T., Wu, W., Peng, Y., Liu, X., Han, Y., Chen, X., Gao, Z., Xia, J., Shao, Z., Greening, C. 2024. A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps. Sci Adv, 10(17), eadl2281.
43) Li, Q., Ma, Z., Huo, J., Zhang, X., Wang, R., Zhang, S., Jiao, J., Dong, X., Janssen, P.H., Ungerfeld, E.M., Greening, C., Tan, Z., Wang, M. 2024. Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield. ISME J, 18(1), wrad016.
42) Yu, M., Zhang, M., Zeng, R., Cheng, R., Zhang, R., Hou, Y., Kuang, F., Feng, X., Dong, X., Li, Y., Shao, Z., Jin, M. 2024. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nat Commun, 15(1), 3228.
41) Zhang, C., Peng, Y., Liu, X., Wang, J., Dong, X. 2024. Deep-sea microbial genetic resources: new frontiers for bioprospecting. Trends Microbiol, 32(4), 321-324.
40) Han, Y.; Zhang, C.; Zhao, Z.; Peng, Y.; Liao, J.; Jiang, Q.; Liu, Q.; Shao, Z.; Dong, X., A comprehensive genomic catalog from global cold seeps. Sci Data 2023, 10, 596.
39) Peng, Y.; Lu, Z.; Pan, D.; Shi, L.-D.; Zhao, Z.; Liu, Q.; Zhang, C.; Jia, K.; Li, J.; Hubert, C. R. J.; Dong, X., Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species. ISME J 2023, 17, 1774–1784.
38) Dong, X., Lan, H., Huang, L., Zhang, H., Lin, X., Weng, S., Peng, Y., Lin, J., Wang, J., Peng, J., Yang, Y., Metagenomic views of microbial communities in sand sediments associated with coral reefs. Microbial ecology 2023, 85(2): 465-477.
37) Zhang, C., Liu, X., Shi, L. D., Li, J., Xiao, X., Shao, Z., Dong, X., Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments. npj Biofilms and Microbiomes 2023, 9(1), 13.
36) Zhang, C.; Fang, Y.-X.; Yin, X.; Lai, H.; Kuang, Z.; Zhang, T.; Xu, X.-P.; Wegener, G.; Wang, J.-H.; Dong, X., The majority of microorganisms in gas hydrate bearing subseafloor sediments ferment macromolecules. Microbiome 2023, 11(1): 37.
35) Xiao, X.; Luo, M.; Zhang, C.; Zhang, T.; Yin, X.; Wu, X.; Zhao, J.; Tao, J.; Chen, Z.; Liang, Q.; Dong, X., Metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments. Microbiology Spectrum 2023, 11(2): e05337-22.
34) Dong, X.; Peng, Y.; Wang, M.; Woods, L.; Wu, W.; Wang, Y.; Xiao, X.; Li, J.; Jia, K.; Greening, C., Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nature Communications 2023, 14(1): 1127.
33) Zhang, H.; Wang, Y.; Liu, P.; Sun, Y.; Dong, X.; Hu, X., Unveiling the occurrence, hosts and mobility potential of antibiotic resistance genes in the deep ocean. Science of The Total Environment 2022, 816, 151539.
32) Shi, L.-D.; Dong, X.; Liu, Z.; Yang, Y.; Lin, J.-G.; Li, M.; Gu, J.-D.; Zhu, L.-Z.; Zhao, H.-P., A mixed blessing of viruses in wastewater treatment plants. Water Research 2022, 215, 118237.
31) Li, J.; Dong, X.; Tang, Y.; Zhang, C.; Yang, Y.; Zhang, W.; Liu, S.; Feng, X.; Shang, L.; Peng, X., Deep sea cold seep is an atmospheric Hg sink and MeHg source. 2022.
30) Jia, K.; Peng, Y.; Chen, X.; Jian, H.; Jin, M.; Yi, Z.; Su, M.; Dong, X.; Yi, M., A novel inovirus reprograms metabolism and motility of marine Alteromonas. Microbiology Spectrum 2022, e03388-22.
29) Dong, X.; Zhang, C.; Peng, Y.; Zhang, H.-X.; Shi, L.-D.; Wei, G.; Hubert, C. R.; Wang, Y.; Greening, C., Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments. Nature Communications 2022, 13, (1), 1-14.
28) Dong, X.; Lan, H.; Huang, L.; Zhang, H.; Lin, X.; Weng, S.; Peng, Y.; Lin, J.; Wang, J.-h.; Peng, J., Metagenomic views of microbial communities in sand sediments associated with coral reefs. Microbial Ecology 2022, 1-13.
27) Bay, S. K.; Dong, X.; Bradley, J. A.; Leung, P. M.; Grinter, R.; Jirapanjawat, T.; Arndt, S. K.; Cook, P. L.; LaRowe, D. E.; Nauer, P. A., Trace gas oxidizers are widespread and active members of soil microbial communities. Nature microbiology 2021, 6, (2), 246-256.
26) Bay, S. K.; Waite, D. W.; Dong, X.; Gillor, O.; Chown, S. L.; Hugenholtz, P.; Greening, C., Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. The ISME journal 2021, 15, (11), 3339-3356.
25) Dong, X.; Zhang, C.; Li, W.; Weng, S.; Song, W.; Li, J.; Wang, Y., Functional diversity of microbial communities in inactive seafloor sulfide deposits. FEMS Microbiology Ecology 2021, 97, (8), fiab108.
24) Li, W. L.; Dong, X.; Lu, R.; Zhou, Y. L.; Zheng, P. F.; Feng, D.; Wang, Y., Microbial ecology of sulfur cycling near the sulfate‐methane transition of deep‐sea cold seep sediments. Environmental Microbiology 2021.
23) Li, Z.; Pan, D.; Wei, G.; Pi, W.; Zhang, C.; Wang, J.-H.; Peng, Y.; Zhang, L.; Wang, Y.; Hubert, C. R., Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. The ISME journal 2021, 15, (8), 2366-2378.
22) Xu, Y.; Teng, Y.; Dong, X.; Wang, X.; Zhang, C.; Ren, W.; Zhao, L.; Luo, Y.; Greening, C., Genome-resolved metagenomics reveals how soil bacterial communities respond to elevated H2 availability. Soil Biology and Biochemistry 2021, 163, 108464.
21) Zhang, C.; Meckenstock, R. U.; Weng, S.; Wei, G.; Hubert, C. R.; Wang, J.-H.; Dong, X., Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition. FEMS Microbiology Ecology 2021, 97, (5), fiab045.
20) Chakraborty, A.; Ruff, S. E.; Dong, X.; Ellefson, E. D.; Li, C.; Brooks, J. M.; McBee, J.; Bernard, B. B.; Hubert, C. R., Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences 2020, 117, (20), 11029-11037.
19) Chiri, E.; Greening, C.; Lappan, R.; Waite, D. W.; Jirapanjawat, T.; Dong, X.; Arndt, S. K.; Nauer, P. A., Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations. The ISME journal 2020, 14, (11), 2715-2731.
18) Dong, X.; Rattray, J. E.; Campbell, D. C.; Webb, J.; Chakraborty, A.; Adebayo, O.; Matthews, S.; Li, C.; Fowler, M.; Morrison, N. M., Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nature communications 2020, 11, (1), 1-14.
17) Jordaan, K.; Lappan, R.; Dong, X.; Aitkenhead, I. J.; Bay, S. K.; Chiri, E.; Wieler, N.; Meredith, L. K.; Cowan, D. A.; Chown, S. L., Hydrogen-oxidizing bacteria are abundant in desert soils and strongly stimulated by hydration. Msystems 2020, 5, (6), e01131-20.
16) Dong, X.; Bäcker, L. E.; Rahmatullah, M.; Schunk, D.; Lens, G.; Meckenstock, R. U., Quantification of microbial degradation activities in biological activated carbon filters by reverse stable isotope labelling. AMB Express 2019, 9, (1), 1-7.
15) Dong, X.; Greening, C.; Rattray, J. E.; Chakraborty, A.; Chuvochina, M.; Mayumi, D.; Dolfing, J.; Li, C.; Brooks, J. M.; Bernard, B. B., Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nature communications 2019, 10, (1), 1-12.
14) Dong, X.; Greening, C.; Brüls, T.; Conrad, R.; Guo, K.; Blaskowski, S.; Kaschani, F.; Kaiser, M.; Laban, N. A.; Meckenstock, R. U., Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. The ISME journal 2018, 12, (8), 2039-2050.
13) Dong, X. Insights into anaerobic degradation of benzene and naphthalene. Technische Universität München, 2017.
12) Dong, X.; Dröge, J.; von Toerne, C.; Marozava, S.; McHardy, A. C.; Meckenstock, R. U., Reconstructing metabolic pathways of a member of the genus Pelotomaculum suggesting its potential to oxidize benzene to carbon dioxide with direct reduction of sulfate. FEMS microbiology ecology 2017, 93, (3).
11) Dong, X.; Jochmann, M. A.; Elsner, M.; Meyer, A. H.; Bäcker, L. E.; Rahmatullah, M.; Schunk, D.; Lens, G.; Meckenstock, R. U., Monitoring microbial mineralization using reverse stable isotope labeling analysis by mid-infrared laser spectroscopy. Environmental science & technology 2017, 51, (20), 11876-11883.
10) Meckenstock, R. U.; Boll, M.; Mouttaki, H.; Koelschbach, J. S.; Tarouco, P. C.; Weyrauch, P.; Dong, X.; Himmelberg, A. M., Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. Microbial Physiology 2016, 26, (1-3), 92-118.
9) Sun, J.; Zhang, Y.; Dong, X.; Chen, M.; Zhou, J., Regeneration of spent NOx scrubber liquor using a dual‐chamber microbial fuel cell. Journal of Chemical Technology & Biotechnology 2015, 90, (9), 1692-1698.
8) Zhang, Y.; Shi, Z.; Chen, M.; Dong, X.; Zhou, J., Evaluation of simultaneous nitrification and denitrification under controlled conditions by an aerobic denitrifier culture. Bioresource Technology 2015, 175, 602-605.
7) Dong, X.; Zhang, Y.; Zhou, J.; Li, H.; Wang, X.; Chen, M., Evaluation of simultaneous reduction of Fe (II) EDTA‐NO and Fe (III) EDTA by a bacterial pure culture. Journal of Chemical Technology & Biotechnology 2014, 89, (1), 111-116.
6) Li, N.; Zhang, Y.; Li, Y.; Chen, M.; Dong, X.; Zhou, J., Reduction of Fe (II) EDTA‐NO using Paracoccus denitrificans and changes of Fe (II) EDTA in the system. Journal of Chemical Technology & Biotechnology 2013, 88, (2), 311-316.
5) Chen, M.; Zhang, Y.; Zhou, J.; Dong, X.; Wang, X.; Shi, Z., Sulfate removal by Desulfovibrio sp. CMX in chelate scrubbing solutions for NO removal. Bioresource technology 2013, 143, 455-460.
4) Dong, X.; Zhang, Y.; Zhou, J.; Chen, M.; Wang, X.; Shi, Z., Fe (II) EDTA–NO reduction coupled with Fe (II) EDTA oxidation by a nitrate-and Fe (III)-reducing bacterium. Bioresource technology 2013, 138, 339-344.
3) Wang, X.; Zhang, Y.; Dong, X.; Chen, M.; Shi, Z.; Zhou, J., Fe (II) EDTA–NO reduction by sulfide in the anaerobic aqueous phase: stoichiometry and kinetics. Energy & fuels 2013, 27, (10), 6024-6030.
2) Zhang, X.; Jin, R.; Liu, G.; Dong, X.; Zhou, J.; Wang, A., Removal of nitric oxide from simulated flue gas via denitrification in a hollow-fiber membrane bioreactor. Journal of Environmental Sciences 2013, 25, (11), 2239-2246.
1) Dong, X.; Zhang, Y.; Zhou, J.; Li, N.; Chen, M., Reduction of Fe (III) EDTA in a NOx scrubber liquor by a denitrifying bacterium and the effects of inorganic sulfur compounds on this process. Bioresource technology 2012, 120, 127-132.
