Representative publications

  1. Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z & Zhou J. 2024. Environmental stress mediates groundwater microbial community assembly. Nature Microbiology 9, 490-501.
  2. Ning D, Yuan M, Wu L, Zhang Y, Guo X, Zhou X, Yang Y, Arkin AP, Firestone MK, and Zhou J. 2020. A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nature Communications 11, 4717. (top 1% highly cited, Web of Science)
  3. Ning D, Deng Y, Tiedje JM, Zhou J. 2019. A General Framework for Quantitatively Assessing Ecological Stochasticity. Proceedings of the National Academy of Sciences of the United States of America 116:16892-16898. (top 1% highly cited, Web of Science)
  4. Wu L, Ning D (co-first author), Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown MR, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A, Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J. 2019. Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology 4:1183–1195. (top 1% highly cited, Web of Science).
  5. Zhou J, Ning D. 2017. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiology and Molecular Biology Reviews 81. (top 1% highly cited, Web of Science)


  1. Shi ZJ, Xiao N, Ning D, Tian R, Zhang P, Curtis D, Nostrand JDV, Wu L, Hazen TC, Rocha AM, He Z, Arkin AP, Firestone MK & Zhou J. 2022. EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline. In revision. (bioRxiv,
  2. Zhang L, Ning D, Mantilla-Calderon D, Chen W, Gao J, Hamilton K, Liu J, Zhou J & Ling F. 2024. In revision.
  3. Su Y, Yang Y, Guo X, Gao Y, Feng J, Wu L, Lei J, Liu S, Gao Q, Qin W, Zeng Y, Liang Z, Yuan M, Ning D, Wu L & Zhou J. 2023. Submitted.
  4. Lei J, Su Y, Jian S, Guo X, Yuan M, Bates CT, Shi Z, Li J, Su Y, Ning D, Wu L, Zhou J & Yang Y. 2023. Submitted.
  5. Deng S, Yang Y, Guo X, Wu L, Yuan MM, Zhang Y, Shi W, Zhou X, Cornell CR, Bates CT, Liu S, Liang Z, Lei J, Gao Q, Ning D, Wu L, Liu X, Luo Y, Tiedje JM & Zhou J. 2024. Submitted.
  6. Shi W, Tian R, Guo X, Ning D, Zhou X, Yuan M, Feng J, Zhou A, Fu Y, Xu G, Hu N, Mu D, Shi P, Fan X, Teng Y, Zhao X, Li Z, Liu J, Wu L, He Z, Nostrand JDV, Liu X, Luo Y, Tiedje JM, Yang Y & Zhou J. 2024. Submitted.
  7. Wu L, Ning D, Zhu C, Tian R, Gao S, Zhang B, Zhao J, Zhang Y, Xiao N, Wang Y, Brown MR, Tu Q, Global Water Microbiome Consortium, Ju F, Wells GF, Guo J, He Z, Nielsen PH, Wang A, Zhang Y, Chen T, He Q, Criddle CS, Wagner M, Tiedje JM, Curtis TP, Wen X, Yang Y, Alvarez-Cohen L, Stahl DA, Alvarez PJJ, Rittmann BE & Zhou J. 2024. Submitted.
  8. Zhu C, Wu L, Ning D, Tian R, Gao S, Zhang B, Zhao J, Zhang Y, Xiao N, Wang Y, Brown MR, Tu Q, Global Water Microbiome Consortium, Ju F, Wells GF, Guo J, He Z, Nielsen PH, Wang A, Zhang Y, Chen T, He Q, Criddle CS, Wagner M, Tiedje JM, Curtis TP, Wen X, Yang Y, Alvarez-Cohen L, Stahl DA, Alvarez PJJ, Rittmann BE & Zhou J. 2024. Submitted.
  9. Fan Y, Ning D, He Z, Zhang P, Rocha AM, Zhang Y, Nostrand JDV, Wu L, Elias DA, Joyner DC, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Yang Y & Zhou J. 2023. In prep.
  10. Zhou J, Xiao N, Ning D, He Q, Leibold MA & Hastings A. 2023. In prep.

Published papers


  1. Michael JP, Putt AD, Yang Y, Adams BG, McBride KR, Fan Y, Lowe KA, Ning D, Jagadamma S, Moon JW, Klingeman DM, Zhang P, Fu Y, Hazen TC & Zhou J. 2024. Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment. Water Research, 121460.
  2. Tao X, Yang Z, Feng J, Jian S, Yang Y, Bates CT, Wang G, Guo X, Ning D, Kempher ML, Liu XJA, Ouyang Y, Han S, Wu L, Zeng Y, Kuang J, Zhang Y, Zhou X, Shi Z, Qin W, Wang J, Firestone MK, Tiedje JM & Zhou J. 2024. Experimental warming accelerates positive soil priming in a temperate grassland ecosystem. Nature Communications 15, 1178.
  3. Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler M-KH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W & Qin W. 2024. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. The ISME Journal 18.


  1. Zhang Y, Ning D, Wu L, Yuan MM, Zhou X, Guo X, Hu Y, Jian S, Yang Z, Han S, Feng J, Kuang J, Cornell CR, Bates CT, Fan Y, Michael JP, Ouyang Y, Guo J, Gao Z, Shi Z, Xiao N, Fu Y, Zhou A, Wu L, Liu X, Yang Y, Tiedje JM & Zhou J. 2023. Experimental warming leads to convergent succession of grassland archaeal community. Nature Climate Change 13, 561-569.
  2. Qin Y, Wu L, Zhang Q, Wen C, Nostrand JDV, Ning D, Raskin L, Pinto A & Zhou J. 2023. Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing. mSystems 8, e01025-01023.
  3. Cornell CR, Zhang Y, Ning D, Xiao N, Wagle P, Xiao X & Zhou J. 2023. Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland. The ISME Journal.
  4. Wu L, Yang Y, Ning D, Gao Q, Yin H, Xiao N, Zhou BY, Chen S, He Q & Zhou J. 2023. Assessing mechanisms for microbial taxa and community dynamics using process models. mLife 2, 239-252.
  5. Liang Q, Zhang J, Ning D, Yu W, Chen G, Tao X, Zhou J, Du Z & Mu D. 2023. Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments. mBio 14, e03535-03522.
  6. Xu T, Tao X, He H, Kempher ML, Zhang S, Liu X, Wang J, Wang D, Ning D, Pan C, Ge H, Zhang N, He Y-X, and Zhou J. 2023. Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia. The ISME Journal.
  7. Shi K, Liang B, Feng K, Ning D, Cornell CR, Zhang Y, Xu W, Zhou M, Deng Y, Jiang J, Liu T, Wang A, and Zhou J. 2023. Electrostimulation triggers an increase in cross-niche microbial associations toward enhancing organic nitrogen wastewater treatment. Journal of Environmental Management 331, 117301.


  1. Wu L, Zhang Y, Guo X, Ning D, Zhou X, Feng J, Yuan MM, Liu S, Guo J, Gao Z, Ma J, Kuang J, Jian S, Han S, Yang Z, Ouyang Y, Fu Y, Xiao N, Liu X, Wu L, Zhou A, Yang Y, Tiedje JM, and Zhou J. 2022. Reduction of microbial diversity in grassland soil is driven by long-term climate warming. Nature Microbiology 7, 1054-1062. (top 1% highly cited, Web of Science)
  2. Xiao N, Zhou A, Kempher ML, Zhou BY, Shi ZJ, Yuan M, Guo X, Wu L, Ning D, Nostrand JV, Firestone MK, and Zhou J. 2022. Disentangling direct from indirect relationships in association networks. Proceedings of the National Academy of Sciences 119, e2109995119. (top 1% highly cited, Web of Science)
  3. Kuang J, Deng D, Han S, Bates CT, Ning D, Shu W, and Zhou J. 2022. Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems. mLife 1, 399-411.
  4. Goff JL, Szink EG, Thorgersen MP, Putt AD, Fan Y, Lui LM, Nielsen TN, Hunt KA, Michael JP, Wang Y, Ning D, Fu Y, Van Nostrand JD, Poole II FL, Chandonia J-M, Hazen TC, Stahl DA, Zhou J, Arkin AP, and Adams MWW. 2022. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments. Environmental Microbiology
  5. Yang L, Ning D, Yang Y, He N, Li X, Cornell CR, Bates CT, Filimonenko E, Kuzyakov Y, Zhou J, Yu G, and Tian J. 2022. Precipitation balances deterministic and stochastic processes of bacterial community assembly in grassland soils. Soil Biology and Biochemistry 168, 108635.
  6. Sun J, Lin Z, Ning D*(corresponding), Wang H, Zhang Z, He Z, and Zhou J. 2022. Functional microbial community structures and chemical properties indicated mechanisms and potential risks of urban river eco-remediation. Science of The Total Environment 803, 149868.
  7. Cornell CR, Zhang Y, Ning D, Wu L, Wagle P, Steiner JL, Xiao X, Zhou J, and Bailey MJ. 2022. Temporal Dynamics of Bacterial Communities along a Gradient of Disturbance in a U.S. Southern Plains Agroecosystem. mBio 13, e03829-03821.
  8. Bates CT, Escalas A, Kuang J, Hale L, Wang Y, Herman D, Nuccio EE, Wan X, Bhattacharyya A, Fu Y, Tian R, Wang G, Ning D, Yang Y, Wu L, Pett-Ridge J, Saha M, Craven K, Brodie EL, Firestone M, and Zhou J. 2022. Conversion of marginal land into switchgrass conditionally accrues soil carbon but reduces methane consumption. The ISME Journal 16, 10-25.
  9. Paradis CJ, Miller JI, Moon JW, Spencer SJ, Lui LM, Van Nostrand JD, Ning D, Steen AD, McKay LD, Arkin AP, Zhou J, Alm EJ, and Hazen TC. 2022. Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater. Ground Water 60, 99-111.
  10. Liu Y, Zeng M, Xie Z, Ning D, Zhou J, Yu X, Liu R, Zhang L, and Fang J. 2022. Microbial Community Structure and Ecological Networks during Simulation of Diatom Sinking. Microorganisms 10, 639.
  11. Aslani F, Geisen S, Ning D, Tedersoo L, and Bahram M. 2022. Towards revealing the global diversity and community assembly of soil eukaryotes. Ecology Letters 25, 65-76.


  1. Chen L, Zhang M, Ning D, Van Nostrand JD, Yang Y, Zhou J, and Zuo J. 2021. Behaviors of Homologous Antibiotic Resistance Genes in a Cephalosporin WWTP, Subsequent WWTP and the Receiving River. Frontiers in Environmental Science 9.
  2. Kuang J, Bates CT, Wan X, Ning D, Deng D, Shu W, and Zhou J. 2021. High historical variability weakens the effects of current climate differentiation on microbial community dissimilarity and assembly. Global Change Biology 27, 5963-5975.
  3. Wang A, Shi K, Ning D, Cheng H, Wang H, Liu W, Gao S, Li Z, Han J, Liang B, and Zhou J. 2021. Electrical selection for planktonic sludge microbial community function and assembly. Water Research 206, 117744.
  4. Huang Z, Hou D, Zhou R, Zeng S, Xing C, Wei D, Deng X, Yu L, Wang H, Deng Z, Weng S, Ning D, Xiao C, Yan Q, Zhou J, He Z, and He J. 2021. Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem. Frontiers in Microbiology 12, 3298.
  5. Sun C, Zhang B, Ning D, Zhang Y, Dai T, Wu L, Li T, Liu W, Zhou J, and Wen X. 2021. Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern. Water Research 200, 117295.
  6. Yuan MM, Guo X, Wu L, Zhang Y, Xiao N, Ning D, Shi Z, Zhou X, Wu L, Yang Y, Tiedje JM, and Zhou J. 2021. Climate warming enhances microbial network complexity and stability. Nature Climate Change 11, 343-348. (top 1% highly cited, Web of Science)
  7. Ceja-Navarro JA, Wang Y, Ning D, Arellano A, Ramanculova L, Yuan MM, Byer A, Craven KD, Saha MC, Brodie EL, Pett-Ridge J, and Firestone MK. 2021. Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. Microbiome 9, 96.
  8. Shi W, Ma Q, Pan F, Fan Y, Kempher ML, Ning D, Qu Y, Wall JD, Zhou A, Zhou J, and Marshall CW. 2021. Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations. mSystems 6, e00493-00421.
  9. Zhang B, Ning D, Van Nostrand JD, Sun C, Yang Y, Zhou J, and Wen X. 2021. The call for regional design code from the regional discrepancy of microbial communities in activated sludge. Environmental Pollution 273, 116487.
  10. Li L, Ning D, Jeon Y, Ryu H, Santo Domingo JW, Kang D-W, Kadudula A, and Seo Y. 2021. Ecological insights into assembly processes and network structures of bacterial biofilms in full-scale biologically active carbon filters under ozone implementation. Science of The Total Environment 751, 141409.
  11. Gao Q, Gao S, Bates C, Zeng Y, Lei J, Su H, Dong Q, Qin Z, Zhao J, Zhang Q, Ning D, Huang Y, Zhou J, and Yang Y. 2021. The microbial network property as a bio-indicator of antibiotic transmission in the environment. Science of The Total Environment 758, 143712.


  1. Zou Y, Ning D (co-first), Huang Y, Liang Y, Wang H, Duan L, Yuan T, He Z, Yang Y, Xue K, Van Nostrand JD, Zhou J. 2020. Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest. Science of The Total Environment 725:138504.
  2. Liang Y, Ning D, Lu Z, Zhang N, Hale L, Wu L, Clark IM, McGrath SP, Storkey J, Hirsch PR, Sun B, and Zhou J. 2020. Century long fertilization reduces stochasticity controlling grassland microbial community succession. Soil Biology and Biochemistry 151, 108023.
  3. Zhang B, Ning D, Van Nostrand JD, Sun C, Yang Y, Zhou J, and Wen X. 2020. Biogeography and Assembly of Microbial Communities in Wastewater Treatment Plants in China. Environmental Science & Technology 54, 5884-5892.
  4. Zhang B, Ning D, Yang Y, Van Nostrand JD, Zhou J, Wen X. 2020. Biodegradability of wastewater determines microbial assembly mechanisms in full-scale wastewater treatment plants. Water Research 169:115276.
  5. Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, Shi W, Wu L, Zhang Y, Yang Y, Adams BG, Rocha AM, Detienne BL, Lowe KA, Joyner DC, Klingeman DM, Arkin AP, Fields MW, Hazen TC, Stahl DA, Alm EJ, Zhou J. 2020. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome 8:51.
  6. Guo X, Gao Q, Yuan M, Wang G, Zhou X, Feng J, Shi Z, Hale L, Wu L, Zhou A, Tian R, Liu F, Wu B, Chen L, Jung CG, Niu S, Li D, Xu X, Jiang L, Escalas A, Wu L, He Z, Van Nostrand JD, Ning D, Liu X, Yang Y, Schuur EAG, Konstantinidis KT, Cole JR, Penton CR, Luo Y, Tiedje JM, and Zhou J. 2020. Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming. Nature Communications 11, 4897.
  7. Gao Q, Wang G, Xue K, Yang Y, Xie J, Yu H, Bai S, Liu F, He Z, Ning D, Hobbie SE, Reich PB, and Zhou J. 2020. Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study. Proceedings of the National Academy of Sciences of the United States of America 117, 33317-33324.
  8. Wu B, Liu F, Zhou A, Li J, Shu L, Kempher ML, Yang X, Ning D, Pan F, Zane GM, Wall JD, Van Nostrand JD, Juneau P, Chen S, Yan Q, Zhou J, and He Z. 2020. Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. The ISME Journal 14, 2862-2876.
  9. Tao X, Feng J, Yang Y, Wang G, Tian R, Fan F, Ning D, Bates CT, Hale L, Yuan MM, Wu L, Gao Q, Lei J, Schuur EAG, Yu J, Bracho R, Luo Y, Konstantinidis KT, Johnston ER, Cole JR, Penton CR, Tiedje JM, and Zhou J. 2020. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. Microbiome 8, 84.
  10. Feng J, Wang C, Lei J, Yang Y, Yan Q, Zhou X, Tao X, Ning D, Yuan MM, Qin Y, Shi ZJ, Guo X, He Z, Van Nostrand JD, Wu L, Bracho-Garillo RG, Penton CR, Cole JR, Konstantinidis KT, Luo Y, Schuur EAG, Tiedje JM, Zhou J. 2020. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. Microbiome 8:3.
  11. Tu Q, Yan Q, Deng Y, Michaletz ST, Buzzard V, Weiser MD, Waide R, Ning D, Wu L, He Z, and Zhou J. 2020. Biogeographic patterns of microbial co-occurrence ecological networks in six American forests. Soil Biology and Biochemistry 148, 107897.
  12. Zhao M, Cong J, Cheng J, Qi Q, Sheng Y, Ning D, Lu H, Wyckoff K, Deng Y, Li D, Zhou J, Zhang Y. 2020. Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China. Forests 11:285.
  13. Dai T, Zhao Y, Ning D, Huang B, Mu Q, Yang Y, Wen D. 2020. Dynamics of coastal bacterial community average ribosomal RNA operon copy number reflect its response and sensitivity to ammonium and phosphate. Environmental Pollution 260:113971.
  14. Huang Z, Zeng S, Xiong J, Hou D, Zhou R, Xing C, Wei D, Deng X, Yu L, Wang H, Deng Z, Weng S, Kriengkrai S, Ning D, Zhou J, He J. 2020. Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome. Microbiome 8:32.
  15. Miao L, Wang P, Hou J, Ning D, Liu Z, Liu S, Li T. 2020. Chronic exposure to CuO nanoparticles induced community structure shift and a delay inhibition of microbial functions in multi-species biofilms. Journal of Cleaner Production 262:121353.


  1. Buzzard V, Michaletz S, Deng Y, He Z, Ning D, Shen L, Tu Q, Nostrand JV, Voordeckers J, Wang J, Weiser M, Kaspari M, Waide R, Zhou J, Enquist B. 2019. Continental scale structuring of forest and soil diversity via functional traits. Nature Ecology & Evolution, 3:1298–1308.
  2. Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Qiu G, Liu X, Luo Y, Tiedje JM, Yang Y, Zhou J. 2019. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nature Ecology & Evolution 3:612-619.
  3. Zhang Z, Deng Y, Feng K, Cai W, Li S, Yin H, Xu M, Ning D, Qu Y. 2019. Deterministic Assembly and Diversity Gradient Altered the Biofilm Community Performances of Bioreactors. Environmental Science & Technology 53:1315-1324.
  4. Zelaya AJ, Parker AE, Bailey KL, Zhang P, Van Nostrand J, Ning D, Elias DA, Zhou J, Hazen TC, Arkin AP, Fields MW. 2019. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Research 164:114917.
  5. Shi Z, Yin H, Van Nostrand JD, Voordeckers JW, Tu Q, Deng Y, Yuan M, Zhou A, Zhang P, Xiao N, Ning D, He Z, Wu L, Zhou J. 2019. Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. mSystems 4:e00296-00219.
  6. Hou L, Mulla SI, Niño-Garcia JP, Ning D, Rashid A, Hu A, Yu C-P. 2019. Deterministic and stochastic processes driving the shift in the prokaryotic community composition in wastewater treatment plants of a coastal Chinese city. Applied Microbiology and Biotechnology 103:9155-9168.
  7. Gao Q, Yang Y, Feng J, Tian R, Guo X, Ning D, Hale L, Wang M, Cheng J, Wu L, Zhao M, Zhao J, Wu L, Qin Y, Qi Q, Liang Y, Sun B, Chu H, Zhou J. 2019. The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil. Global Ecology and Biogeography 28:1093-1105.
  8. Feng K, Zhang Y, He Z, Ning D, Deng Y. 2019. Interdomain ecological networks between plants and microbes. Molecular Ecology Resources 19:1565-1577.
  9. Weiser MD, Ning D, Buzzard V, Michaletz ST, He Z, Enquist BJ, Waide RB, Zhou J, Kaspari M. 2019. Thermal disruption of soil bacterial assemblages decreases diversity and assemblage similarity. Ecosphere 10:e02598.


  1. Guo X, Feng J, Shi Z, Zhou X, Yuan M, Tao X, Hale L, Yuan T, Wang J, Qin Y, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Ning D, Liu X, Luo Y, Tiedje JM, Yang Y, Zhou J. 2018. Climate warming leads to divergent succession of grassland microbial communities. Nature Climate Change 8:813-818.
  2. Chen C, Hemme C, Beleno J, Shi ZJ, Ning D, Qin Y, Tu Q, Jorgensen M, He Z, Wu L, Zhou J. 2018. Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy. The ISME Journal 12:1210.
  3. He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J. 2018. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. mBio 9:e02435-17.
  4. Deng Y, Ning D, Qin Y, Xue K, Wu L, He Z, Yin H, Liang Y, Buzzard V, Michaletz ST, Zhou J. 2018. Spatial scaling of forest soil microbial communities across a temperature gradient. Environmental Microbiology 20:3504-3513.
  5. Whitman T, Neurath R, Perera A, Chu-Jacoby I, Ning D, Zhou J, Nico P, Pett-Ridge J, Firestone M. 2018. Microbial community assembly differs across minerals in a rhizosphere microcosm. Environmental Microbiology 20:4444-4460.
  6. Brandon AM, Gao S-H, Tian R, Ning D, Yang S-S, Zhou J, Wu W-M, Criddle CS. 2018. Biodegradation of Polyethylene and Plastic Mixtures in Mealworms (Larvae of Tenebrio molitor) and Effects on the Gut Microbiome. Environmental Science & Technology 52:6526-6533. (top 1% highly cited, Web of Science)
  7. Wu B, Liu F, Weiser MD, Ning D, Okie JG, Shen L, Li J, Chai B, Deng Y, Feng K, Wu L, Chen S, Zhou J, He Z. 2018. Temperature determines the diversity and structure of N2O-reducing microbial assemblages. Functional Ecology 32:1867-1878.
  8. Yang S-S, Brandon AM, Andrew Flanagan JC, Yang J, Ning D, Cai SY, Fan HQ, Wang ZY, Ren J, Benbow E, Ren N-Q, Waymouth RM, Zhou J, Criddle CS, Wu W-M. 2018. Biodegradation of polystyrene wastes in yellow mealworms (larvae of Tenebrio molitor Linnaeus): Factors affecting biodegradation rates and the ability of polystyrene-fed larvae to complete their life cycle. Chemosphere 191:979-989.
  9. Yang S-S, Wu W-M, Brandon AM, Fan H-Q, Receveur JP, Li Y, Wang Z-Y, Fan R, McClellan RL, Gao S-H, Ning D, Phillips DH, Peng B-Y, Wang H, Cai S-Y, Li P, Cai W-W, Ding L-Y, Yang J, Zheng M, Ren J, Zhang Y-L, Gao J, Xing D, Ren N-Q, Waymouth RM, Zhou J, Tao H-C, Picard CJ, Benbow ME, Criddle CS. 2018. Ubiquity of polystyrene digestion and biodegradation within yellow mealworms, larvae of Tenebrio molitor Linnaeus (Coleoptera: Tenebrionidae). Chemosphere 212:262-271.
  10. Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM, Zhou J. 2018. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass. Frontiers in Microbiology 9.


  1. Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, Qin Y, Xue K, Wu L, He Z, Voordeckers JW, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Yang Y, Brown JH. 2017. Correspondence: Reply to ‘Analytical flaws in a continental-scale forest soil microbial diversity study’. Nature Communications 8:15583.
  2. Yan Q, Stegen JC, Yu Y, Deng Y, Li X, Wu S, Dai L, Zhang X, Li J, Wang C, Ni J, Li X, Hu H, Xiao F, Feng W, Ning D, He Z, Van Nostrand JD, Wu L, Zhou J. 2017. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Molecular Ecology 26:3839-3850.
  3. Kaspari M, Bujan J, Weiser MD, Ning D, Michaletz ST, He Z, Enquist BJ, Waide RB, Zhou J, Turner BL, Wright SJ. 2017. Biogeochemistry drives diversity in the prokaryotes, fungi, and invertebrates of a Panama forest. Ecology 98:2019-2028.
  4. Liu J, Techtmann SM, Woo HL, Ning D, Fortney JL, Hazen TC. 2017. Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil. Scientific Reports 7:5762.
  5. Wen C, Wu L, Qin Y, Van Nostrand JD, Ning D, Sun B, Xue K, Liu F, Deng Y, Liang Y, Zhou J. 2017. Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform. PLoS One 12:e0176716.
  6. Zhou M, Zhang X, Yang X, Zhang Y, He H, Ning D. 2017. Flavobacterium ardleyense sp. nov., isolated from Antarctic soil. International Journal of Systematic and Evolutionary Microbiology 67:3996-4001.
  7. Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, Qin Y, Xue K, Wu L, He Z, Voordeckers JW, Nostrand JDV, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Yang Y, Brown JH. 2016. Temperature mediates continental-scale diversity of microbes in forest soils. Nature Communications 7:12083. (top 1% highly cited, Web of Science)

Before 2015

  1. Ning D, Huang Y, Pan R, Wang F, Wang H. 2014. Effect of eco-remediation using planted floating bed system on nutrients and heavy metals in urban river water and sediment: A field study in China. Science of The Total Environment 485:596-603.
  2. Ning D, Wang H. 2012. Involvement of Cytochrome P450 in Pentachlorophenol Transformation in a White Rot Fungus Phanerochaete chrysosporium. PLOS ONE 7:e45887.
  3. Ning D, Wang H, Zhuang Y. 2010. Induction of functional cytochrome P450 and its involvement in degradation of benzoic acid by Phanerochaete chrysosporium. Biodegradation 21:297-308.
  4. Ning D, Wang H, Ding C, Lu H. 2010. Novel evidence of cytochrome P450-catalyzed oxidation of phenanthrene in Phanerochaete chrysosporium under ligninolytic conditions. Biodegradation 21:889-901.
  5. Ning D, Wang H, Wang L, Ding C. 2009. Induction and function of cytochrome P450 in degradation of refractory organic chemicals by Phanerochaete chrysosporium. China Environmental Science:407-412.
  6. Ning D, Wang H, Li D. 2009. Induction and measurement of cytochrome P450 in white rot fungi. Environmental Science-Chinese 30:2485-2490.
  7. Ning D, Wang H, Zhuang Y, Li D. 2007. Inducement and degradation function of P450 in Phanerochaete chrysosporium by in situ spectroscopic analysis. Chemical Journal of Chinese Universities-Chinese 28:1469-1474.
  8. Hou J, Qu Y, Ning D, Wang H. 2014. Impact of human exposure factors on health risk assessment for benzene-contaminated site. Environmental Science & Technology-Chinese 8.
  9. Hou J, Qu Y, Ning D, Wang H. 2014. Characteristic of human exposure factors in china and their uncertainty analysis in health risk assessment. Environmental Science & Technology-Chinese 8.
  10. He F, Wang L, Ning D, Guo G, Wang H. 2012. Phenanthrene biodegradation and dynamic change of expression of naphthalene dioxygenase (ndo) genes in a halophilic bacteria consortium. China Environmental Science 32:1662-1669.
  11. Weng P, Ning D, Wang H, Wang F, Jiang D. 2012. Comparison of urban river oxygenation by water transfer and aeration in plain area. Journal of Changzhou University (Natural Science Edition) 2:40-44.
  12. Zeng B, Ning D, Wang H. 2008. Preliminary study on biodegradation of pentachlorophenol by white rot fungus. Environmental Chemistry 27:181-185.
  13. Wei M, Wang H, Liu C, Ning D. 2008. Bioaugmentation with immobilized genetically engineered microorganism (GEM)/CAS process for treatment of atrazine wastewater. Environmental Science-Chinese 29:1555-1560.
  14. Jiang J, Wang H, Gao J, Song L, Ning D. 2008. Cloning and sequence analysis of 1,2,4-trichlorobenzene dioxygenase and dehydrogenase genes. Environmental Science-Chinese 29:1655-1659.
  15. Wei J, Wang L, Ning D, Wei D, Hu H. 2004. Effect of dechlorination on reduction of biotoxication of disinfected wastewater. China Water & Wastewater 20:16-19.
  16. Wei J, Hu H, Ning D, Wang L, Wei D. 2004. Study on bio-toxicity of disinfection byproduct after chlorination/dechlorination in wastewater. China Water & Wastewater 20:5-8.
  17. Wei J, Hu H, Ning D, Wang L, Wei D. 2004. Effect of wastewater characteristics on acute toxicity incurred by disinfection. China Water & Wastewater 20:17-20.

updated 2024.3.21