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  1. Buzzard, V., S. T. Michaletz, Y. Deng, Z. He, D. Ning, L. Shen, Q. Tu, J. Van Nostrand, J. W. Voordeckers, J. Wang, M. D. Weiser, M. Kaspari, R. B. Waide, J.-Z. Zhou, and B. J. Enquist. Continental scale structuring of forest and soil diversity via functional traits. 2019. Nature Ecol. & Evol. 3:1298-1308.  Suppl Material: File 1 (csv), File 2 (csv), File 3 (csv), File 4 (zip), File 5 (pdf)
  2. Dai J, Y Liu, S Li u, S Li, N Gao, J Wang, J Zhou and D Qiu. 2019. Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteinsBMC Microbiol. 19:173 Suppl Material
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  6. Gao, Q., Y. Yang, J. Feng, R. Tian, X. Guo, D. Ning, L. Hale, M. Wang, J. Cheng, L. Wu, M. Zhao, J. Zh ao, L .Wu, Y. Qin, Q. Qi, Y. Liang, B. Sun, H. Chu, and J.-Z. Zhou. 2019. The spatial scale-dependency of diazotrophic and bacterial community assembly in paddy soilGlob Ecol Biogeography, Suppl Material (docx)
  7. Gao, S., J. Ho, L. Fan, A. Nouwens, R. D. Hoelzle, B. Schulz, J. Guo, J.-Z. Zhou, Z. Yuan, and P. L. Bond. 2019. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acidSci Tot Environ, 672:625-633. Suppl Material
  8. Guo X, X Zhou, L Hale, M Yuan, D Ning, J Feng, Z Shi, Z Li, B Feng, Q Gao, L Wu, W Shi, A Zhou, Y Fu, L Wu, Z He, JD Van Nostrand, G Qiu, X Liu, Y Luo, JM Tiedje, Y Yang, and JZ Zhou. 2019. Climate warming accelerates temporal scaling of grassland soil microbial biodiversityNat Ecol Evol., 3:612-619.
  9. Hale, L., W. Feng, H. Yin, X. Guo, X. Zhou, R. Bracho, E. Pegoraro, C. R. Penton, L. Wu, J. Cole, K. T. Konstantinidis, Y. Luo, J. M. Tiedje, E. A. G. Schuur, and J.-Z. Zhou. 2019. Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbonISME J. Suppl Material
  10. Hu Y, Z Zhang, L Huang, Q Qi, L Liu, Y Zhao, Z Wang, H Zhou, X Lv, Z Mao, Y Yang, J Zhou, and P Kardol. 2019. Shifts in soil microbial community functional gene structure across a 61-year desert revegetation chronosequenceGeoderma. 347:126-134. Suppl Material (docx)
  11. Huang RL, SP McGrath, PR Hirsch, IM Clark, J Storkey, LY Wu, JZ Zhou, and Liang YT. 2019. Plant-microbe networks in soil are weakened by century-long use of inorganic fertilizersMicrobial Biotechnol. 12:1464-1475.
  12. Johnston, E. R., J.  K. Hatt, Z. He, L. Wu, X. Guo; Y. Luo, E. A. G Schuur, J. M. Tiedje, J.-Z. Zhou, and K. T. Konstantinidis. 2019. Responses of tundra soil microbial communities to half a decade of experimental in-situ warming at two critical depthsProc. Nat. Acad. Sci. 116:15096-15105. Suppl Material (pdf); Suppl Data 1 (txt)2 (txt)3 (txt)4 (txt)
  13. Li Y, B Zhang, K Wang, Q Tu, B Cui, B Ren, J He, X Shen, JD Van Nostrand, J Zhou, W Shi, L Xiao, C Lu, X Zhou, and Y Yao. Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planusInt J Oral Sci. 11:3. Suppl Material (docx)
  14. Liang B, JC Ma, WW Cai, ZL Li, WZ Liu, MY Qi, YK Zhao, XD Ma, Y Deng, AJ Wang, and JZ Zhou. 2019. Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulationWat Res. 148:398-406. Suppl Material (docx)
  15. Ma X, Q Zhang, M Zheng, Y Gao, T Yuan, L Hale, JD Van Nostrand, JZ Zhou, S Wan and Y Yang. 2019. Microbial functional traits are sensitive indicators of mild disturbance by lamb grazing. ISME J., 13:1370-1373. Suppl Material (docx)
  16. Ning D, Y Deng, JM Tie dje, and J Zhou. 2019. A general framework for quantitatively assessing ecological stochasticityProc Nat Acad Sci. 116:16893-16898.
  17. Pegoraro E, M Mauritz, R Bracho, C Ebert, P Dijkstra, BA Hungate, KT Konstantinidis, Y Luo, C Schädel, JM Tiedje, J Zhou, and EAG Schuur. 2019. Glucose addition increases the magnitude and decreases the age of soil respired carbon in a long-term permafrost incubation studySoil Biol Biochem. 129:201-211. Suppl Material 1 (docx) Suppl Material 2 (xml)
  18. Shi X, J Zhao, L Chen, J Zuo, Y Yang, Q Zhang, Z Qin, and J Zhou. 2019. Genomic dynamics of full-scale temperature-phased anaerobic digestion treating waste activated sludge: Focusing on temperature differentiation. Waste Manag. 87:621-628.
  19. Shi Z, H Yin, JD Van Nostran d, JW Voordeckers, Q Tu, Y Deng, M Yuan, A Zhou, P Zhang, N Xiao, D Ning, Z He, L Wu, and J Zhou. 2019. Functional gene array-based ultrasensitive and quantitative detection of microbial populations in complex communitiesmSystems. 4:e00296-19. Suppl Material: Text (pdf), GeoChip 5 Table (pdf), Tables/Figures (pdf)
  20. Song, D., X. Chen, M. Xu, R. Hai, A. Zhou, R. Tian, J. D. Van Nostrand, M. L. Kempher, J. Guo, G. Sun, and J.-Z. Zhou. 2019. Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River SedimentFront Microbiol, doi: 10.3389/fmicb.2019.02263. Suppl Material (zip)
  21. Tang L, L Zhong, K Xue, S Wang, Z Xu, Q Lin, C Luo, Y Rui, X Li, M Li, W Liu, Y Yang, J Zhou, and Y Wang. 2019. Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grasslandSoil Biol Biochem. 134:113-121. Suppl Material (docx)
  22. Tian J, AJ Dunga it, X Lu, Y Yang, IP Hartley, W Zhang, J Mo. G Yu, J Zhou, and Y Kuzyakov. Long‐term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil. Glob Change Biol. 25:3267-3281. Suppl Material (docx)
  23. Wakelin S, P Maclean , V Cave, J Zhou, GA Grelet, adn D Whitehead. 2019. Characterising the soil ecosystem phenotype associated with relatively low nitrate-N concentrationsAppl Soil Sci. 142:189-198. Suppl Material: Text (docx), Data (xlsx)
  24. Wang P, Y Chen, Y Sun, S Tan, S Zhang, Z Wang, JZ Zhou, G Zhang, W Shu, C Luo, and J Kuang. 2019.  Distinct biogeography of different fungal guilds and their associations with plant species richness in forest ecosystems. Front Ecol Evol. 7:216, doi: 10.3389/fevo.2019.00216. Suppl Info (zip)
  25. Wang XB, J Yao, HY Zhang, XG Wang, KH Li, XT Lu, ZW Wang, JZ Zhou, and XG Han. 2019. Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslandsSci Tot Environ. 654:960-968. Suppl Material (docx)
  26. Wang Y, H Zheng, F Chen, Y Yang, J Zeng, J Van Nostrand, JZ Zhou, and Z Ouyang. 2019. Artificial reforestation produces less diverse soil nitrogen-cycling genes than natural restoration. Ecosphere. 10:e02562. Suppl Material (pdf)
  27. Weiser MD, D Ning, V Buzzard, ST Michaletz, Z He, BJ Enquist, RB Waide, JZ Zhou, and M Kaspari. 2019. Thermal disruption of soil bacterial assemblages decreases diversity and assemblage similarityEcosphere, Suppl Material (pdf)
  28. Wu L, D Ning, B Zhang, Y Li, P Zhang, X Shan, Q Zhang, M Brown, Z Li, JD Van Nostrand, F Ling, N Xiao, Y Zhang, J Vierheilig, GF Wells, Y Yang, Y Deng, Q Tu, A Wang, Global Water Microbiome Consortium, T Zhang, Z He, J Keller, PH Nielsen, PJJ Alvarez, CS Criddle, M Wagner, JM Tiedje, Q He, TP Curtis, DA Stahl, L Alvarez-Cohen, BE Rittmann, X Wen, and JZ Zhou. 2019. Global diversity and biogeography of the bacterial communities in wastewater treatment plantsNat Microbiol, 4:1183-1195. Suppl Material: Tables S1S3S11S12
  29. Xia X, Y Wang , Y Yang, T Luo, JD Van Nostrand, J Zhou, N Jiao, R Zhang . Ocean acidification regulates the activity, community structure and functional potential of heterotrophic bacterioplankton in an oligotrophic gyreJ Geophys Res: Biogeosci. 124:1001-1017. Suppl MaterialNormalized Miicroarray Data (zip)
  30. Yang S, Q Zheng, Myuan, Z Shi, NR Chiariello, KM Docherty, S Dong, CB Field, Y Gu, J Gutknecht, BA Hungate, X Le Roux, X Ma, A Niboyet, T Yuan, J Zhou, and Yu Yang. 2019. Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentialsSci Tot Environ. 652:1474-1481. Suppl Material (doc)
  31. Zelaya AJ, AE Pa rker, KL Bailey, P Zhang, JD Van Nostrand, D Ning, DA Elias, J Zhou, TC Hazen, AP Arkin, and MW Fields. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquiferWater Res. 164:114917. Suppl Material (pdf)
  32. Zhang Q, M Wang, X Ma, Q Gao, T Wang, X shi, J Zhou, J Zuo, and Y Yang. 2019. High variations of methanogenic microorganisms drive full-scale anaerobic digestion processEnviron Internat. 126:543-551. Suppl Material (docx)
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  34. Zhao M, X Lu, H Zhao, Y Yang, L Hale, Q Gao, W Liu, J Guo, Q Li, J Zhou, and F Wan. 2019. Ageratina adenophora invasions are associated with microbially mediated differences in biogeochemical cyclesSci Tot Environ. 677:47-56. Suppl Material (docx)
  35. Zhao M, B Sun, L Wu, F Wang, C Wen, M Wang, Y Liang, L Hale, J Zhou, and Y Yang. 2019. Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changesMol Ecol. 28:1842-1856. Suppl Material (docx)
  36. Zhu CM, JY Zhang, R Guan, L Hale, N Chen, M Li, ZH Lu, QY Ge, YF Yang, JZ Zhou, and T Chen. 2019. Alternate succession of aggregate-forming cyanobacterial genera correlated with their attached bacteria by co-pathwaysSci Total Environ 688:867-879. Suppl Material (zip)
  1. Brandon AM, S Ga o, R Tian, D Ning, S Yang, J Zhou, W Wu, and CS Criddle. 2018. Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiomeEnviron. Sci Technol52:6526-6533. Suppl Material (pdf)
  2. Chen C, C Hemme, J Beleno, ZJ Shi, D Ning, Y Qin, Q Tu, M Jorgenson, Z He, L Wu, and J Zhou. 2018. Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapyISME J. 12:1210–1224. Suppl Material (pdf)
  3. Christensen GA, J Moon, AM Veach, JJ Mosher, AM Wymore, JD Van Nostrand, J Zhou, TC Hazen, AP Arkin, and DA Elias. 2018. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm compositionPLoS ONE 13(3): e0194663. Suppl Material (zip)
  4. Deng Y, D Ning, Y Qin, K Xue, L Wu, Z He, H Yin, Y Liang, V Buzzard, ST Michaletz, and J Zhou. 2018. Spatial scaling of forest soil microbial communities across a temperature gradientEnviron Microbiol. 20:3504-3513. Supplemental Information; Supplmental Data: R code R fileSuppl Material (pdf) 
  5. Dignam BEA , O’Callaghan M, Condron LM, Kowalchuk GA, Van Nostrand JD, Zhou J, and SA Wakelin. 2018. Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppressionPLoS ONE 13: e0196581. Suppl Material (zip)
  6. Guo X, J Feng, Z Shi, X Zhou, M Yuan, X Tao, L Hale, T Yuan, J Wang, Y Qin, A Zhou, Y Fu, L Wu, Z He, J Van Nostrand, D Ning, X Liu, Y Luo, J Tiedje, Y Yang, and J Zhou. 2018. Climate warming leads to divergent succession of grassland microbial communitiesNat Clim Change. 8:813-818. Suppl Material (pdf)
  7. Guo X, X Zhou, L Hale, M Yuan, D Ning, Z Shi, Y Qin, F Liu, L Wu, Z He, J Van Nostrand, X Liu, Y Luo, JM Tiedje, and J Zhou. Taxonomic and functional responses of soil microbial communities to annual removal of aboveground plant biomass. Front. Microbio. 9:954. Suppl. Material. (zip)
  8. He J, Q Tu, Y Ge, Y Qin, B Cui, X Hu, Y Wang, Y Deng, K Wang, JD Van Nostrand, J Li, J Zhou, Y Li, X Zhou. 2018. Taxonomic and functional analyses of the supragingival microbiome from caries-affected and caries-free hosts.Microbial Ecol. 75:543-554. Suppl Material: Figures (doc), Tables (xls)
  9. He Z, P Zhang, L Wu, AM Rocha, Q Tu, Z Shi, B Wu, Y Qin, J Wang, Q Yan, D Curtis, JD Van Nostrand, L Wu, Y Yang, DA Elias, DB Watson, MWW Adams, MW Fields, EJ Alm, TC Hazen, PD Adams, AP Arkin, and J-Z Zhou. 2018. Microbial functional gene diversity predicts groundwater contamination and ecosystem functioningmBio. 9:e02435-17. Supplementary Information (csv)Suppl Material (pdf)
  10. Hou Y, C Yang, A Zhou, W Liu, C Liu, W Cai, J Zhou, and J Zhou. 2018. Microbial community response and SDS-PAGE reveal possible mechanism of waste activated sludge acidification enhanced by microaeration coupled thermophilic pretreatmentProcess Biochem. 64:1-8. Suppl Material (doc)
  11. Karna RR, GM Hettiarachchi, JD Van Nostrand, T Yuan, CW Rice, YM Assefa, and J Zhou. Microbial population dynamics and the role of sulfur reducing bacteria genes in stabilizing Pb, Zn and Cd in the terrestrial subsurface. Soil Systems. 2:60. 
  12. Li H, Z X u, Q Yan, S Yang, JD Van Nostrand, Z Wang, Z He, J Zhou, Y Jiang, and Y Deng. Soil microbial beta-diversity is linked with compositional variation in aboveground plant biomass in a semi-arid grassland. Plant Soil. 423:465-480. Suppl Material (pdf)
  13. Li Y, Y Li, SX Chang, Y Yang, S Fu, P Jiang, Y Luo, M Yang, Z Chen, S Hu, M Zhao, X Liang, Q Xu, G Zhou, and J Zhou. 2018. Biochar reduces soil heterotrophic respiration in a subtropical plantation through increasing soil organic carbon recalcitrancy and decreasing carbon-degrading microbial activity.Soil Biol Biochem. 122:173-185. Suppl Material (doc)
  14. Liang J, J Xia , Z Shi, L Jiang, S Ma, X Lu, M Mauritz, SM Natali, E Pegoraro, CR Penton, C Plaza, VG Salmon, G Celis, JR Cole, KT Konstantinidis, JM Tiedje, J Zhou, EAG Schuur, and Y Luo. 2018. Biotic responses buffer warming‐induced soil organic carbon loss in Arctic tundraGlob Change Biol. 24:4946-4959. Suppl Material (doc)
  15. Liang J, Z Zhou, C Huo, Z Shi, JR Cole, L Huang, KT Konstantinidis, X Li, B Liu, Z Luo, CR Penton, EA Schuur, JM Tiedje, YP Wang, L Wu, J Xia, J Zhou, and Y Luo. 2018. More replenishment than priming loss of soil organic carbon with additional carbon inputNat Comm. 8:3175. Suppl Material: Figures (pdf), Tables (xls)
  16. Reyes VC, PB Gedalanga , N Merino, JD Van Nostrand, SP Keely, SK De Long, J Zhou, and S Mahendra. 2018. Differential sensitivity of wetland-derived nitrogen cycling microorganisms to copper nanoparticlesACS Sustainable Chem Eng. 6:11642-11652. Suppl Material (pdf)
  17. Sheng Z, JD Van Nostrand, J Zhou, and Y Liu. 2018. Contradictory effects of silver nanoparticles on activated sludge wastewater treatment. J Haz Mat. 341:448-456.
  18. Shi S, DJ Herman, Z He, J Pett-Ridge, L Wu, J Zhou, and MK Firestone. Plant roots alter microbial functional genes supporting root litter decompositionSoil Biol Biochem. 127:90-99. Suppl Material (doc)
  19. Shi Z, Y Lin, KR Wilcox, L Souza, L Jiang, J Jiang, CG Jung, X Xu, M Yuan, X Guo, L Wu, J Zhou, and Y Luo. Successional change in species composition alters climate sensitivity of grassland productivityGlob Change Biol. 24:4993-5003. Suppl Material (doc)
  20. Tian J, N He, L Hale, S Niu, G Yu, Y Liu, E Blagodatskaya, Y Kuzyakov, Q Gao, and J Zhou. 2018. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold-temperate forestsFunct Ecol. 32:61-70. Suppl Material (pdf)
  21. Tian J, N He, W Kong, Y Deng, K Feng, SM Green, X Wang, J Zhou, Y Kuzyakov, and G Yu. 2018. Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities. Soil Biol Biochem. 123:80-86. Suppl Material (doc)
  22. Vishnivetska ya TA, H Hu, JD Van Nostrand, AM Wymore, X Xu, G Qiu, X Feng, J Zhou, SD Brown, CC Brandt, M Podar, B Gu and DA Elias. 2018. Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, ChinaEnviron. Sci. Process Impacts. 20:673.  Suppl Material (pdf)
  23. Wang M, J Ding , B Sun, J Zhang, KN Wyckoff, H Yue, M Zhao, Y Liang, X Wang, C Wen, J Zhou, and Y Yang. Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stabilityEnviron Microbiol. 20:2509-2522. Suppl Material (doc)
  24. Weiser, M., S. Michaletz, V. Buzzard, Y. Deng, Z. He, L. Shen, B. Enquist, R. Waide, J.-Z. Zhou, and M. Kaspari. 2018. Toward a theory for diversity gradients: the abundance-adaptation hypothesis. Ecography. 41:255-264.
  25. Weiser M D, NG Swenson, BJ Enquist, ST Michaletz, RB Waide, J Zhou, and M Kaspari. 2018. Taxonomic decomposition of the latitudinal gradient in species diversity of North American floras. J Biogeography. 45:418–428. Suppl Material: Appendix 1 (doc), Appendix 2 (csv)
  26. Whitman T, R Neurath, A Perera, I Chu‐Jacoby, D Ning, J Zhou, P Nico, J Pett‐Ridge, and M Firestone. Microbial community assembly differs across minerals in a rhizosphere microcosmEnviron Microbiol. Suppl Material: Figures (doc), Table 1 (xls), Table 2 (xls)
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  31. Xue K, J Zhou, J Van Nostrand, M Mench, C Bes, L Giagnoni, and G Renella. 2018. Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree standEnviron Poll. 242(A):229-238. Suppl Material (doc)
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  1. Cheng L, N Zhang , M Yuan, J Xiao, Y Qin, Y Deng, Q Tu, K Xue, J Van Nostrand, L Wu, Z He, X Zhou, MB Leigh, K Konstantinidis, E Schuur, Y Luo, J Tiedje, and J Zhou.2017. Warming enhances old organic carbon decomposition through altering functional microbial communitiesISME J. 11:1825-1835. doi: 10.1038/ismej.2017.48. Suppl Material: Appendix 1 (pdf); Appendix 2 (xlsx); Figures (pdf)
  2. Colin Y, O Nicolitch, JD Van Nostrand, JZ Zhou, MP Turpault, S Uroz. 2017. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequenceSci Rep. 7:9604. Doi:10.1038/s41598-017-07639-1. Suppl Material
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  4. Feng W, Liang J, Hale LE, Jung CG, Chen J, Zhou J, Xu M, Yuan M, Wu L, Bracho R, Pegoraro E, Schuur EAG, and Luo Y. 2017. Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warmingGlob Change Biol. Suppl Material: Figure S1 (tif); Figure S2 (tif); Method (pdf)
  5. Gu Y, JD Van Nostrand, L Wu, Z He, Y Qin, F Zhao, and J Zhou. 2017. Bacterial communities and arsenic functional genes diversity in arsenic contaminated soils from different geographic locationsPloS One, 12(5): e0176696.  Supplementary Data: Fasta files (zip)Suppl Material (docx)
  6. Hou Y, B Zhang , H Yun, Z Yang, J Han, J Zhou, A Wang, and H Cheng. Palladized cells as suspension catalyst and electrochemical catalyst for reductively degrading aromatics contaminants: Roles of Pd size and distribution. Wat Res.
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  8. Kaspari, M ., Bujan, J., Weiser, M. D., Ning, D., Michaletz, S. T., Zhili, H., Enquist, B. J., Waide, R. B., Zhou, J., Turner, B. L. and Wright, S. J. 2017. Biogeochemistry drives diversity in the prokaryotes, fungi, and invertebrates of a Panama forestEcology. 98:2019-2028. Suppl Material (pdf)
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  12. Li P, Z Jiang, Y Wang, Y Deng, JD Van Nostrand, T Yuan, H Liu, D Wei, and J Zhou. 2017. Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwaterWater Res. 123:268-276. Suppl Material (docx)
  13. Lindsay, MR, C Anderson, N Fox, G Scofield, J Allen, E Anderson, L Bueter, S Poudel, K Sutherland, JH Munson-McGee, JD Van Nostrand, J Zhou, JR Spear, BK Baxter, DR Lageson, and ES Boyd. Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, UtahGeobiology. 15:131-145. DOI: 10.1111/gbi.12201. Suppl Material (docs)
  14. Lyles, CN, VA Parisi, W H Beasley, JD Van Nostrand, J Zhou, and JM Suflita. Elucidation of the methanogenic potential from coalbed microbial communities amended with volatile fatty acidsFEMS Microbiol Ecol 93(4):fix040 doi: 10.1093/femsec/fix040. Suppl Material (zip)
  15. Ma, X., Zhao, C., Gao, Y., Liu, B., Wang, T., Yuan, T., Hale, L., Van Nostrand, J. D., Wan, S., Zhou, J. and Yang, Y. Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and depositionMol Ecol. 26:4186-4196. Suppl Material (docx)
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  22. Wang, X., X. Lü, J. Yao, Z. Wang, Y. Deng, W. Cheng, J.-Z. Zhou, X. Han. 2017. Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylandsISME J. 11:1345-1358. Suppl Material (doc)
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  24. Wen C, L Wu, Y Qin, JD Van Nostrand, S Bo, K Xue, Y Deng, F Liu, and J Zhou. 2017. Evaluation of the Reproducibility of Amplicon Sequencing with Illumina MiSeq PlatformPLoS One, 12(4):e0176716. doi: 10.1371/journal.pone.0176716. Suppl Material (zip)
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  26. Wu L, Y Yang , S Wang, H Yue, Q Lin, Y Hu, Z He, JD Van Nostrand, L Hale, X Li, JA Gilbert, and J Zhou. 2017. Alpine soil carbon is vulnerable to rapid microbial decomposition under climate coolingISME J. 11:2102-2111. Suppl Material (doc)
  27. Xu T, Y Li, Z He, JD Van Nostrand, and J Zhou. Cas9 nickase-assisted RNA repression enables stable and efficient manipulation of essential metabolic genes in Clostridium cellulolyticum. Front. Microbiol. 8:1744. doi: 10.3389/fmicb.2017.01744. Suppl Material (pdf)
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  29. Yan Z, Y He, H Cai, J Van Nostrand, Z He, J Zhou, L Krumholz, H Jiang. 2017. Interconnection of key microbial functional genes for enhanced benzo[a]pyrene biodegradation in sediments by microbial electrochemistry. Environ Sci Technol. 51:8519-8529. Suppl Material (pdf)
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  50. Zhang Y, Q Yang, J Ling, JD Van Nostrand, Z Shi, J Zhou, J Dong. 2016. The shifts of diazotrophic communities in spring and summer associated with coral Galaxea astreata, Pavona decussata and Porites luteaFront. Microbiol. 7:1870. Suppl Material (pdf)
  51. Zhao M, B Sun, L Wu, Q Gao, F Wang, C Wen, M Wang, Y Liang, L Hale, J Zhou, and Y Yang. 2016. Zonal soil type determines soil microbial responses to maize cropping and fertilizationmSystems. 1(4):e00075-16. DOI: 10.1128/mSystems.00075-16. Suppl Material (pdf)
  52. Zhou JZ, Y Deng, L Shen, C Wen , Q Yan, D Ning, Y Qin, K Xue, L Wu, Z He, JW Voordeckers, JD Van Nostrand, V Buzzard, ST Michaletz, BJ Enquist, MD Weiser, M Kaspari, R Waide, Y Yang, JH Brown. 2016. Temperature mediates continental-scale diversity of microbes in forest soilsNat Comm. 7:12083. doi:10.1038/ncomms12083. Supplementary Data: OTU Table (zip)Suppl Material (pdf)
  53. Zhu YG, JQ Su , Z Cao, K Xue, J Quensen, GX Guo, YF Yang, J Zhou, HY Chu, and JM Tiedje. 2016. A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation. Sci. Bull. 61:1052-1061. Suppl Material (doc)
  54. Zhang, Y., J. Cong, H. Lu, Y. Deng, X. Liu, J.-Z. Zhou, and D. Li. 2016. Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient. Scientific report, 6: article number 28819; DOI: 10.1038/srep28819.
  1. Azarbad, H, A., M. Niklińska, R. Laskowski, N. van Straalen, C. van Gestel, J.-Z. Zhou, Z. He, C. Wen, and W. Röling. 2015. Microbial community composition and functions are resilient to metal pollution along two forest soil gradientsFEMS Microbiology Ecology, 91:1-11, Suppl Material (zip)
  2. Cai, M., Y. Nie, C. Chi, Y. Tang, Y. Li, X. Wang, Z. Liu, Y. Yang, J.-Z. Zhou, and X. L. Wu. 2015. Crude oil as a microbial seed bank with unexpected functional potentials. Sci. Reports, 5:16057, doi:10.1038/srep16057. Suppl Material (pdf)
  3. Cong J, Y Yang, X Liu, H Lu, X Liu, J-Z Zhou, D Li, H Yin, J Ding, and Y Zhang. 2015. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest successionScientific Reports. 5:10007. Suppl Material (doc)
  4. Dai, J, H Wei, C Tian, FH Damron, J-Z Zhou, and D Qiu. 2015. An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensisBMC Microbiol 15:34, doi:10.1186/s12866-015-0357-0. Suppl Material (doc)
  5. Deng, J, Y Gu, J Zhang, K Xue, Y Qin, M Yuan, H Yin, Z He, L Wu, EAG Schuur, JM Tiedje, and J-Z Zhou. 2015. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in AlaskaMol Ecol. 24:222-234. Suppl Material (doc)
  6. Ding, J., Y. Zhang, Y. Deng, C. Yang, T. Yuan, J. D Van Nostrand, D. Li, J.-Z. Zhou, and Yunfeng Yang. 2015. Integrated metagenomics and network analysis of soil microbial community of the forest timberlineScientific Reports, 5:7994, doi10.1038/srep07994. Suppl Material (pdf)
  7. Ding J, Y Zhang, MM Wang, X Sun, J Cong, Y Deng, H Lu, T Yuan, JD Van Nostrand, D Li, J-Z Zhou and Y Yang. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.Mol Ecol. 24: 5175-5185. Suppl Material (doc)
  8. Dopheide, A, G Lear, Z He, J-Z Zhou, GD Lewis. 2015. Functional gene composition, diversity and redundancy in microbial stream biofilm communitiesPLOS One, 10(4): e0123179. Suppl Material (zip)
  9. Hemme CL, Q Tu, Z Shi, Y Qin, W Gao, Y Deng, JD Van Nostrand, L Wu, Z He, PSG Chain, S Green Tringe, MW Fields, E Rubin, JM. Tiedje, TC Hazen, A Arkin, J-Z Zhou. 2015. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front in Microbiol, Suppl Material (pdf)
  10. Huang C, Z Li, F Chen, Q Liu, Y Zhao, J-Z Zhou, and A Wang. 2015. Microbial community structure and function in response to the shift of sulfide/nitrate loading ratio during the denitrifying sulfide removal processBioresource Technol. 197:227-234. Suppl Material (pdf)
  11. Huang, C, Y Zhao, Z Lia, Y Yuan, C Chen, W Tan, S Gao, L Gao, J-Z Zhou, A Wang. 2015. Enhanced elementary sulfur recovery with sequential sulfate-reducing, denitrifying sulfide-oxidizing processes in a cylindrical-type anaerobic baffled reactorBioresource Tech. 192:478-785.
  12. Leigh, M. B., W.M. Wu, E. Cardenas, O. Uhlik, S. Carroll, T. Gentry, T. L. Marsh, J.-Z. Zhou, P. Jardine, C. S. Ceiddle, J. M. Tiedje. 2015. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probingFront. Environ. Sci. Engineer., 9:453-464, DOI 10.1007/s11783-014-0721-6
  13. Li X, PL Bond, JD Van Nostrand, J-Z Zhou and L Huang. 2015. From lithotroph- to organotrophdominant: directional shift of microbial community in sulphidic tailings during phytostabilizationSci Reports. 5:12978, DOI: 10.1038/srep12978. Suppl Material (pdf)
  14. Liang, J, D Li, Z Shi, JM Tiedje, J-Z Zhou, EAG Schuur, KT Konstantinidis, and Y Luo. 2015. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluationSoil Biol Biochem. 80:127-135. Suppl Material (pdf)
  15. Liang Y, Y Jiang, F Wang, C Wen, Y Deng, K Xue, Y Qin, Y Yang, L Wu, J-Z Zhou and B Sun. 2015. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnoverISME J. 9:2561-2572. Suppl Material (pdf)
  16. Liang Y, Wu L, Clark IM, Xue K, Yang Y, Van Nostrand JD, Deng Y, He Z, McGrath S, Storkey J, Hirsch PR, Sun B, Zhou J. 2015. Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversitymBio6(2):e00240-15. doi:10.1128/mBio.00240-15. Suppl Material (pdf)
  17. Liang, Y, X Zhang, J-Z Zhou, and G Li. 2015. Long-term oil contamination increases deterministic assembly processes in soil microbesEcol Applications.25:1235-1243. Supplementary Information (xls)
  18. Lin, J, J Chen, J He, J Chen, Q Yan, J-Z Zhou, and P Xie. 2015. Effects of microcystin-LR on bacterial and fungal functional genes profile in rat gutToxicon. 96:50-56. Suppl Material (doc), 
  19. Liu, S., Wang, K. Xue, B. Sun, Y. Zhang, Z. He, J. D. Van Nostrand, J.-Z. Zhou and Y. Yang. The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry, Env. Microbiol. 17:566-576. Suppl Material (doc)
  20. Ma, J, Y Deng, T Yuan, J-Z Zhou, and PJJ Alvarez. 2015. Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycleEnviron Poll. 198:154-160. Suppl Material (doc)
  21. MacDonald, CA, MJ Crawley, DJ Wright, J Kuczynski, L Robinson, R knight, WA Al-Soud, SJ Sorenson, Y Deng, J-Z Zhou, and BK Singh. 2015. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment. Environ. Microbiol. 17:841-854. Suppl Material (doc)
  22. Michaletz ST, MD Weiser, J-Z Zhou, M Kaspari, BR Helliker, and BJ Enquist. 2015. Plant Thermoregulation: Energetics, Trait–Environment Interactions, and Carbon EconomicsTrends in Ecol Evol. 30:714-724. Suppl Material (pdf)
  23. Myung J, WM Galega, JD Van Nostrand, T Yuan, J-Z Zhou, and CS Criddle. Long-term cultivation of a stable Methylocystis-dominated methanotrophic enrichment enabling tailored production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate)Biores Technol. 198:811-818.
  24. Myung J, Z Wang, T Yuan, P Zhang, JD Van Nostrand, J-Z Zhou, and CS Criddle. 2015. Production of nitrous oxide from nitrite in stable Type II methanotrophic enrichments. Environ Sci Technol. 49:10969-10975. Suppl Material (pdf)
  25. Penton, CR, D St. Louis, A Pham, JR Cole, L Wu, Y Luo, EAG Schuur, J-Z Zhou and JM Tiedje. 2015. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Front. Microbiol.6:746. Doi:10.3389/fmicb.2015.00746.  Suppl Material (pdf)
  26. Qu, Y, Q Ma, J Deng, W Shen, X Zhang, Z He, JD Van Nostrand, J Zhou, and J-Z Zhou. 2015. Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems. Environ Sci Technol49:4627-4635. Suppl Material (pdf)
  27. Qu Y, X Zhang, Q Ma, J Deng, Y Deng, JD Van Nostrand, L Wu, Z He, Y Qin, J Zhou, and J-Z Zhou. 2015. Microbial community dynamics and activity link to indigo production from indole in bioaugmented activated sludge systemsPLoS ONE, 10(9): e0138455. Suppl Material (pdf)
  28. Saxena, G., E. M. Marzinelli, N. N. Naing, Z. He, Y. Liang, Y. Piceno, S. Mitra, H. Ping, U. M. Joshi, S.Reuben, K. C. Mynampati, S. Mishra, S. Umashankar, .J.-Z. Zhou, G. Andersen, S. Kjelleberg, and S. Swarup. 2015. Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacityEnviron. Sci & Tech., 49:1462-1472. Suppl Material (pdf)
  29. Sheng, Z, JD Van Nostrand, J-Z Zhou, and Y Liu. 2015. The effects of silver nanoparticles on intact wastewater biofilms. Front. Microbiol. 6:680. doi: 10.3389/fmicb.2015.00680. Suppl Material (pdf)
  30. Shi S, E Nuccio, DJ Herman, R Rijkers, K Estera, J Li, U Nunes da Rocha, Z He, J Pett-Ridge, EL Brodie, J-Z Zhou, and M Firestone. 2015. Successional trajectories of rhizosphere bacterial communities over consecutive seasonsmBio6(4):e00746-15. Suppl Material (pdf)
  31. Shi Y, P Grogan, H Sun, J Xiong, Y Yang, J-Z Zhou, H Chu. 2015. Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communitiesSoil Biol Biochem. 86:126-1347. Suppl Material (doc)
  32. Smith MB, AM Rocha, CS Smillie, SW Olesen, C Paradis, L Wu, JH Campbell, JL Fortney, TL Mehlhorn, KA Lowe, JE Earles, J Phillips, SM Techtmann, DC Joyner, DA Elias, KL Bailey, RA Hurt Jr, SP Preheim, MC Sanders, J Yang, MA Mueller, S Brooks, DB Watson, P Zhang, Z He, EA Dubinsky, PD Adams, AP Arkin, MW Fields, J-Z Zhou, EJ Alm, TC Hazen. 2015. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 6: e00326-15. Suppl Material (pdf)
  33. Su, J. Q., L.J. Ding, K. Xue, H. Y. Yao, J. Quensen, S. Bai, W. X. Wei, J.S. Wu, J.-Z. Zhou, J. M. Tiedje, and Y.G. Zhu. 2015. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soilMol. Ecol., 24:136-150. Suppl Material (doc)
  34. Trivedi, P., I.J. Rochester, C. Trivedi, J.D. Van Nostrand, J.-Z. Zhou, S. Karunaratne, I.C. Anderson, B.K. Singh. 2015. Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communitiesSoil Biol Biochem. 91: 169-181. Suppl Material (pdf)
  35. Tu, Q., M. Yuan, Z. He, Y. Deng, K. Xue, L. Wu, S. Hobbie, P. Reich, and J.-Z. Zhou. 2015. Fungal communities respond to long-term elevated CO2 by community reassembly. Appl. Environ. Microbiol., 81:5445-2454. Suppl Material (pdf)
  36. Wang F, Y Liang, Y Jiang, Y Yang, K Xue, J Xiong, J-Z Zhou, and B Sun. 2015. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cyclingSci Rep. 5:14345. Suppl Material (pdf)
  37. Wang, M., S. Liu, F. Wang, B. Sun, J.-Z. Zhou., and Y. Yang. 2015. Microbial responses to southward and northward Cambisol soil transplantMicrobiologyOpen, 4:931-940. Suppl Material (doc)
  38. Wang, X, JD Van Nostrand, Y Deng, X Lu, C Wang, J-Z Zhou and X Han. 2015. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiol Ecol. 91(12). doi: 10.1093/femsec/fiv133. Suppl Material (zip) 
  39. Wang Y, R Zhang, Q Zheng, Y Deng, JD Van Nostrand, J-Z Zhou, and N Jiao. 2015. Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysisICES J Mar Sci. 73:865-875.  Suppl Material (zip)
  40. Wei, STS, MA Fernandez-Martinez, Y Chan, JD Van Nostrand, A de los Rios-Murillo, JMY Chiu, AM Ganeshram, SC Cary, J-Z Zhou, and SB Pointing. 2015. Diverse metabolic and stress-tolerance pathways in chasmoendolithic and soil communities of Miers Valley, McMurdo Dry Valleys, AntarcticaPolar Biol. 38:433-443
  41. Wood, S. A., M. Almaraz, M. A. Bradford, K. L. McGuire, S. Naeem, C. Neill, C. A. Palm, K. L. Tully, and J.-Z. Zhou. 2015. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agricultureFrontiers in Microbiology, 6:90. doi: 10.3389/fmicb.2015.00090. Suppl Material (doc)
  42. Wood, S.A., M. A. Bradford, J. A. Gilbert, K. L. McGuire, C. A. Palm, K. L. Tully, J.-Z. Zhou, and S. Naeem. 2015. Agricultural intensification and the functional capacity of soil microbes on smallholder African farmsJ. Applied Ecol. 52:744-752. Suppl Material (doc)
  43. Wu L, C Wen, Y Qin, H Yin, Q Tu, JD Van Nostrand, T Yuan, M Yuan, Y Deng, and J-Z Zhou. 2015. Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiol. 15:125. DOI 10.1186/s12866-015-0450-4. Suppl Material: Figures, Tables, Methods (pdf); Tables 2 (xls)
  44. Xiong, J, Z He, S Shi, A Kent, Y Deng, L Wu, JD Van Nostrand, and J-Z Zhou. 2015. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystemScientific Reports. 5:9316. Suppl Material (pdf)
  45. Xu M, Z He, Q Zhang, J Liu, J Guo, G Sun, and J-Z Zhou. 2015. Responses of aromatic-degrading microbial communities to elevated nitrate in sediments.Environ Sci Technol 49:12422–12431. Suppl Material (pdf)
  46. Xu, T., Y. Li, Z. Shi, C.L. Hemme, Y. Li, Y. Zhu, J.D. Van Nostrand, Z. He, and J.-Z. Zhou. 2015. Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 NickaseAppl. Environ. Microbiol. 81:4423–4431. Suppl Material (pdf)
  47. Xue K, JD Van Nostrand, J Vangronsveld, N Witters, JO Janssen, J Kumpiene, G Siebielec, R Galazka, L Giagnoni, M Arenella, JZ Zhou, G Renella. 2015. Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil. Chemosphere, 138:469-477. Suppl Material (doc)
  48. Yan Q, Y Bi, Y Deng, Z He, L Wu, JD Van Nostrand, Z Shi, J Li, X Wang, Z Hu, Y Yu, and J-Z Zhou. 2015. Impacts of the Three Gorges Dam on microbial structure and potential functionSci Rep 5:8605. doi:10.1038/srep08605. Suppl Material (pdf)
  49. Yang, C., Y. Li, B.Y. Zhou, Y. Zhou, W. Zheng, Y. Tian, J.D. Van Nostrand, L. Wu, Z. He, J.-Z. Zhou, and T. Zheng. 2015. Illumina sequencing-based analysis of bacterial community dynamics during Akashiwo sanguine bloom in Xiamen sea, ChinaSci Rep, 5: doi:10.1038/srep08476. 
  50. Yin H, J Niu, Y Ren, J Cong, X Zhang, F Fan, Y Xiao, X Zhang, J Deng, M Xie, Z He, J-Z Zhou, Y Liang, and X Liu. 2015. An integrated insight into the response of sedimentary microbial communities to heavy metal contaminationSci Rep. 5:14266. Suppl Material: Figures (pdf); Tables (xls)
  51. Yue, H., M. Wang, S. Wang, J. A. Gilbert, X. Sun, L. Wu, Q. Lin, Y. Hu, X. Li, Z. He, J.-Z. Zhou, and Y. Yang. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslandsISME J, 9:2012-2020. Suppl Material (doc)
  52. Zhang, P, JD Van Nostrand, Z He, R Chakraborty, Y Deng, D Curtis, M Fields, TC Hazen, AP Arkin, and J-Z Zhou. A slow-release substrate stimulates groundwater microbial communities for long-term in-situ Cr(VI) reduction. Eviron Sci Technol. 49:12922-12931. Suppl Material (pdf)
  53. Zhang, P, WM Wu, JD Van Nostrand, Y Deng, Z He, T Gihring, G Zhang, CW Schadt, D Watson, P Jardine, CS Criddle, S Brooks, TL Marsh, JM Tiedje, AP Arkin, and J-Z Zhou. 2015. Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reductionAppl Environ Microbiol. 81:4164-4172. Suppl Material (pdf)
  54. Zhang, Y, J Cong, H Lu, G Li, Y Xue, Y Deng, H Li, J-Z Zhou and D Li. 2015. Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, ChinaMicrobial Biotech. 8:739-746. Supplementary Data: Fastq files (zip) - ForwardReverseBarcodesSuppl Material (doc)
  55. Zhang, Y., J. Ling, Q.S. Yang, C. Q. Wen, Q.Y. Yan, H.Y. Sun, J. Van Nostrand, Z. Shi, J.-Z. Zhou, J.D. Dong. 2015. The functional gene composition and metabolic potential of coral-associated microbial communitiesSci Report. 5: 16191. Suppl Material (pdf)
  56. Zhang, Y, Z Tian, M Liu, ZJ Shi, L Hale, J-Z Zhou, and M Yang. 2015. High concentrations of the antibiotic spiramycin in wastewater lead to high abundance of ammonia-oxidizing archaea in nitrifying populationsEnviron Sci Technol. 49:9124-9132. Suppl Material (pdf)
  57. Zhang, Z, H Wang, J-Z Zhou, H Li, Z He, JD Van Nostrand, Z Wang, and X Xu. 2015. Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilizationHydrobiolia. 743:221-235. Suppl Material (doc)
  58. Zhou, A, KL Hillesland, Z He, W Schackwitz, Q Tu, GM Zane, Q Ma, Y Qu, DA Stahl, JD Wall, TC Hazen, MW Fields, AP Arkin, and J-Z Zhou. 2015. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgarisISME J. 9:2360-2372. Suppl Material (pdf)
  59. Zhou, J., Z. He, Y. Yang, Y. Deng, S.G. Tringe and L. Alvarez-Cohen. 2015. High-throughput metagenomic technologies for complex microbial community analysis: Open and closed formats. mBio, 6:1e02288-14
  1. Antony-Babu, S., A. Deveau, J. D Van Nostrand, J.-Z. Zhou, F. L. Tacon, C. Robin, P. Frey-Klett, S. Uroz. 2014. Selection of specific bacterial communities by the Black truffle Tuber melanosporum during its development and ascocarp maturationEnviron. Microbiol., 16:2831-2847. Supplementary Data: GeoChip data (xls); Suppl Material: Tables1 (xls), Tables2 (xls), Figures and Tables (pdf)
  2. Bartley, L, T Xu, C Zhang, H Nguyen, and J-Z Zhou. 2014. Switchgrass biomass content, synthesis, and biochemical conversion to biofuels. In: H Luo, Y Wu, and C Kole (eds) Compendiou of Bioenergy Plants: Switchgrass. CRC Press
  3. Chen, Y., J. S. Pettis, M. Corona, W. Chen, C. Li, M. Spivak, P. K. Visscher, G. DeGrandi-Hoffman, H. Boncristiani, Y. Zhao, D. van Engelsdorp, K. Delaplane, L. Solter, F. Drummond, M. Kramer, W. I. Lipkin , G. Palacios, M. C. Hamilton, B. Smith, S. Huang, H. Zheng, J. Li , X. Zhang, A. Zhou, L. Wu, J.-Z. Zhou, M.-L. Lee, E. W. Teixeira, Z. Li, JD. Evans. 2014. Israeli acute paralysis virus: epidemiology, pathogenesis and implications for honey bee healthPLoS Pathogens, 10(7):e1004261.  Suppl Material (zip)
  4. Chen Y, N Qin, J Guo, G Qian, D Fang, D Shi, M Xu, F Yang, Z He, JD Van Nostrand, T Yuan, Y Deng, J-Z Zhou and L Li. 2014. Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosisBMC Genomics. 15:753. Suppl Material (pdf)
  5. Chu, H., S. Wang, H. Yue, Q. Lin, Y. Hu, X. Li, J.-Z. Zhou and Y. Yang. Contrasting soil microbial community structures in two major landscapes of the Tibetan alpine meadowMicrobiology Open, 3(5):585-594. Suppl Material (doc)
  6. Deng, Y and Z He. 2014. Microarray data analysis. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  7. Diaz, M. R., J. D. Van Nordstrand, G.P. Eberli, A. M. Piggot, J.-Z. Zhou, and J. S. Klaus. 2014. Functional Gene Diversity of Oolitic Sands from Great Bahama BankGeobiology, 12: 231-249. Suppl Material (pdf)
  8. Gao, Y. S. Wang, D. Xu, H. Yu, L. Wu, Q. Lin, Y. Hu, X. Li, Z. He, Y. Deng, J.-Z. Zhou, and Y. Yang. 2014. GeoChip as a Metagenomics Tool to Analyze the Microbial Gene Diversity along an Elevation GradientGenomics Data, 2:132-134. Supplementary Data: Microarray data (txt)
  9. He, Z.; J. Xiong, A. D Kent, Y. Deng, K. Xue, G. Wang, L. Wu, J. D Van Nostrand, and J.-Z. Zhou. 2014. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystemISME J 8:714-726. Suppl Material (pdf)
  10. He, Z and J-Z Zhou. 2014. Microarrays for microbial community analysis at a glance. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  11. Hillesland, KL, S Lim, JJ Flowers, S Turkarslan, N Pinel, GM Zane, N Elliott, Y Qin, L Wu, NS Baliga, J-Z Zhou, JD Wall and DA Stahl. 2014. Erosion of functional independence early in the evolution of a microbial mutualismProc Nat Acad Sci USA. 111(4):14822-14827. Suppl Material (pdf)
  12. Jia, X., X. Zhou, Y. Luo, K Xue, X. Xue, X. Xu, Y. Yang, L. Wu, and J.-Z. Zhou. 2014. Effects of substrate addition on soil respiratory carbon release under long-term warming and clipping in a tallgrass prairiePLosOne, 9:e114203, doi: 10.1371/journal.pone.0114203
  13. Kappell, A.D., Y. Wei, R. J. Newton, J. D. Van Nostrand, J.-Z. Zhou, S. L. McLellan, and K. R. Hristova. 2014. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spillFront. Microbiol., 5:205. Supplementary Data: Microarray Data (xlsx)Suppl Material (pdf)
  14. Kuramae, E.E., J. Z. Zhou, G. A. Kowalchuk, and J. A. van Veen. 2014. Soil-borne microbial functional structure across different land usesScientific World J. vol. 2014, Article ID 216071, 8 pages, doi:10.1155/2014/216071
  15. Levy, O., B. A. Ball, B. Bond-Lamberty, K. S. Cheruvelil, A. O. Finley, N. Lottig, S. W. Punyasena, J. Xiao, J.-Z. Zhou, L. B. Buckley, C. T. Filstrup, T. Keitt, J. R. Kellner12, Alan K. Knapp, A. D. Richardson, C. Stow, D. Tcheng, M. Toomey, R. Vargas, J. W. Voordeckers, T. Wagner, and J. W. Williams. 2014. Approaches for advancing scientific understanding of macrosystems. Front. Ecol. Environ. 12: 15–23. Suppl Material (pdf)
  16. Li, X., J. Rui, J. Xiong, J. Li, Z. He, J.-Z. Zhou, A. C. Yannarell, and R. I. Mackie. 2014. Functional potential of soil microbial communities 1 in the maize rhizospherePlosOne, DOI: 10.1371/journal.pone.0112609, 9(11):e112609. Suppl Material (zip)
  17. Li Y, J He, Z He, Y Zhou, M Yuan, X Xu, F Sun, C Liu, J Li, W Xie, Y Deng, Y Qin, JD Van Nostrand, L Xiao, L Wu, J-Z Zhou, W Shi, and X Zhou. 2014. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J. 8:1879-1891. Suppl Material ( pdf)
  18. Li, Y., T. Xu, T. J. Tschaplinski, N. L. Engle, Y. Yang, D. E. Graham, Z. He, and J.-Z. Zhou. 2014. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviationBiotechnol Biofuels., 7:25. DOI: 10.1186/1754-6834-7-25. Suppl Material (pdf)
  19. Liang, B., H. Cheng, J. D. Van Nostrand, J. Ma, H. Yu, D. Kong, W. Liu, N. Ren, L. Wu, A. Wang, D. Lee, and J.-Z. Zhou. 2014. Microbial Community Structure and Function of Nitrobenzene Reduction Biocathode in Response to Carbon Source SwitchoverWater Res., 54:137-48. Suppl Material (docx)
  20. Liang Y, H Zhao, X Zhang, J-Z Zhou, and G Li. 2014. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sitesSci Tot Environ. 487:272-278.
  21. Luo, C., L. M. Rodriguez-R, E. R. Johnston, L. Wu, L. Cheng, K. Xue, Q. Tu, Y. Deng, Z. He, J. Z. Shi, M. M. Yuan, S. A. Rebecca, D. Li, Y. Luo, E. A.G. Schuur, P. Chain, J. M. Tiedje, J.-Z. Zhou, and K. T. Konstantinidis. 2014. Soil microbial community responses to a decade of warming as revealed by comparative metagenomicsAppl. Environ. Microbiol. 80: 1777-1786. Suppl Material (pdf)
  22. Paula, F. S., J. L. M. Rodrigues, J.-Z. Zhou, L. Wu, R. C. Mueller, B. S. Mirza, B. J. M. Bohannan, Klaus Nüsslein, Y. Deng, J. M. Tiedje, and V. H. Pellizari. 2014. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communitiesMol. Ecol. 23:2988-2999. Supplementary Data: Microarray data (xlsx)Suppl Material (pdf)
  23. Probst, AJ, PY Lum, B John, EA Dubinsky, YM Piceno, LM Tom, GL Andersen, Z He and TZ DeSantis. 2014. Microarray of 16S rRNA gene probes for quantifying population differences across microbiome samples. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  24. Qin, Q.L., B. Xie, X. Zhang, X. Chen, B. Chen, J.-Z. Zhou, A. Oren, and Y. Zhang. 2014. A proposed genus boundary for the prokaryotes based on genomic insightsJ. Bacteriol. 96: 2210-2215. Suppl Material (pdf)
  25. Singh, B., C. Quince, C. A. Macdonald, A. Khachane, W. A. Al-Soud, N. Thomas, S. J Sørensen, Z. He, D. White, A.Sinclair, B. Crooks J.-Z. Zhou and C. D. Campbell. 2014. Loss of microbial biodiversity in soils is coincident with reductions in some specialized functionsEnviron. Microbiol. 16(8):2408-2402. Suppl Material (pdf)
  26. Sun, Y., Y. Shen, P. Liang, J.-Z. Zhou, Y. Yang and X. Huang, 2014, Linkages between microbial functional potential and wastewater constituents in large-scale membrane bioreactors for municipal wastewater treatmentWater Research, 56: 162-171. Suppl Material (pdf)
  27. Tu, Q, Y Deng, J-Z Zhou, and Z He. 2014. Development and evaluation of functional gene arrays with GeoChip as an example. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  28. Tu, Q., H. Yu, Z. He, Y. Deng, L. Wu, J. D. Van Nostrand, A. Zhou, J. Voordeckers, Y.-J. Lee, Y. Qin, C. Hemme, Z. Shi, K. Xue, T. Yuan, A. Wang, and J.-Z. Zhou. 2014. GeoChip 4: a functional gene arrays-based high throughput environmental technology for microbial community analysis. Mol. Ecol. Resource 14(5):914-928. Supplementary Data: Microarray data (zip)List of gene families (xlsx)Suppl Material (doc)
  29. Tu, Q., Z. He, Y. Li, Y. Chen, Y. Deng, L. Lin, C. L. Hemme, T. Yuan, J. D. Van Nostrand, L. Wu, X. Zhou, W. Shi, L. Li, J. Xu, and J.-Z. Zhou. 2014. Development of HuMiChip for Functional Profiling of Human MicrobiomesPLoSOne, 9: e90546. doi:10.1371/journal.pone.0090546. Supplementary data: HumiChip data (zip)Suppl Material (zip)
  30. Tu, Q., Z. He, and J.-Z. Zhou. 2014. Strain/Species identification in metagenomes using genome-specific markersNucl. Acid Res., 42: E67-E67 (Editor picks by Genomeweb). Suppl Material (zip)
  31. Van Nostrand J and J-Z Zhou. 2014. Applications of functional gene microarrays for profiling microbial communities. In, V Garcia-Canas, A Cifuentes, and C Simo, eds, Comprehensive Analytical Chemistry: Applications of Advanced Omics Technologies: From Genes to Metabolites, Elsevier, Amsterdam, The Netherlands
  32. Van Nostrand, JD and J-Z Zhou. 2014. GeoChip applications in bioremediation studies. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  33. Varrone*, C., J. D. Van Nostrand*, W. Liu, B. Y. Zhou, Z. Wang, F. Liu, Z. He, L. Wu, J.-Z. Zhou, and A. Wang. 2014. Metagenomic-based analysis of biofilm communities for electrohydrogenesis: From wastewater to hydrogen. Intl. J. of Hydrogen Energy. 39: 222-4233 (*Equal contribution) Suppl Material (docx)
  34. Vigneron, A, P Cruaud, P Pignet, J-C Caprais, N Callac, M Ciobanu, A Godfroy, EG Roussel, BA Cragg, RJ Parkes, JD Van Nostrand, Z He, J-Z Zhou, and L Toffin. 2014. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin.PLOS One, 9(8): e104427. Suppl Material (zip)
  35. Wakelin, S. E. Gerard, A. Black, K. Hamonts, L. Condron, T. Yuan, J. van Nostrand, J.-Z. Zhou, and Maureen O’Callaghan. 2014. Mechanisms of pollution induced community tolerance in a soil microbial community exposed to CuEnvironmental Pollution, 190: 1-9.
  36. Wang, C, X Wang, D Liu, H Wu, X Lu, Y Fang, W Cheng, W Luo, P Jiang, J Shi, H Yin, J-Z Zhou, X Han and E Bai. 2014. Aridity threshold in controlling ecosystem nitrogen cycling in arid and semi-arid grasslandsNature Comm. 5:4799. DOI: 10.1038/ncomms5799. Suppl Material (pdf)
  37. Wang, F. J.-Z. Zhou, and B. Sun. 2014. Structure of functional ecological networks of soil microbial communities for nitrogen transforming and its response to cropping in major soils in Eastern China. Chinese Science Bulletin, 59: 387-396 (In Chinese)
  38. Wang, X., X. Yu, X. Wen, Y. Yang, and J.-Z. Zhou. 2014. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip. PLoS One, 9: e93422. doi:10.1371/journal.pone.0093422. Suppl Material (doc)
  39. Xia, Y., X. Wang, X. Wen, K. Ding, J.-Z. Zhou, Y. Yang, and Y. Zhang. 2014. Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors, Appl. Microbiol. Biotechnol. DOI: 10.1007/s00253-014-5791-7, 98(16):7233-7242. Suppl Material (pdf)
  40. Xu, M., Q. Zhang, C. Xia, Y. Zhong, G. Sun, J. Guo, T. Yuan, J.-Z. Zhou, and Z. He. 2014. Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments. ISME J. 8:1932-1944. Suppl Material (pdf)
  41. Xu, T., Y. Li, Z. He, and J.-Z. Zhou. 2014. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis in Clostridium cellulolyticum. Mol. Microbiol., 91: 694-705. Suppl Material (docx)
  42. Xu, T., Y. Li, J. D. Van Nostrand, Z. He, and J.-Z. Zhou. 2014. Cas9-Based Tools for Targeted Genome Editing and Transcriptional ControlAppl. Environ. Microbiol. 80: 1544-1552. (Review) Suppl Material (pdf)
  43. Xu, X, C Chen, A Wang, H Yu, X Zhou, H Guo, Y Yuan, D Lee, J-Z Zhou, N Ren. 2014. Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input. J Haz Mat 278:250-257. Suppl Material (docx)
  44. Xue, K Z He, JD Van Nostrand, and J-Z Zhou. 2014. GeoChip analysis of soil microbial community responses to global change. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
  45. Xue, K., J. D. Van Nostrand, Z. He and J.-Z. Zhou. 2014. Functional Molecular Analysis of Microbial Nitrogen Cycle by Microarray-based GeoChip: Insights for Climate Change, Agriculture and Other Ecological Studies. In: D. Marco (ed) Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications. Caister Academic, Poole, UK. (out Sept. 2014)
  46. Yang F, Ning K, X. Chang, X. Yuan, Q. Tu, Y. Tong, Y. Deng, C. L. Hemme, J. Van Nostrand, X. Cui, Z. He, Z. Chen, D. Guo, J. Yu, Y. Zhang, J.-Z. Zhou, and J. Xu. 2014. Saliva microbiota carry caries-specific functional gene signatures.PLoS One, 9(2):e76458  Supplementary Data: HumiChip data (xls)Suppl Material (zip)
  47. Yang, Y., Y. Gao, Q. Lin, D. Xu, H. Yu, L. Wu, Y. Hu, X. Li, Z. He, Y. Deng, S. Wang and J.-Z. Zhou. 2014. The microbial gene diversity along an elevation gradient of the Tibetan grasslandISME J, 8: 430-440. Suppl Material (pdf)
  48. Yu, H, C Chen, J Ma, W Liu, J-Z Zhou, D Lee, N Ren, A Wang. 2014. GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification processJ Environ Sci. 26:1375-1382.
  49. Yuan, Y, C Chen, B Liang, C Huang, Y Zhao, X Xu, W Tan, X Zhou, S Gao, D Sun, D Lee, J-Z Zhou, and A Wang. 2014. Fine-tuning key parameters of an integrated reactor system for the simultaneous removal of COD, sulfate and ammonium and elemental sulfur reclamationJ Haz Mat. 269:56-67.  Suppl Material (doc)
  50. Zhang, Y, J Cong, H Lu, G Li, Y Qu, X Su, J-Z Zhou, and D Li. 2014. Community structure and elevational diversity patterns of soil AcidobacteriaJ Environ Sci.26(8):1717-1724. Suppl Material (doc)
  51. Zhang Y., J. Cong, H. Lu, C. Yang, Y. Yang, J.-Z. Zhou, and D. Li. 2014. An integrated study to analyze soil microbial community structure and metabolic potential in two forest typesPLoS One, 9: e93773. doi:10.1371/journal.pone.0093773. Suppl Material (zip)
  52. Zhao, J, J Zuo, X Wang, J Lin, Y Yang, J-Z Zhou, H Chu, and P Li. 2014. GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatantWater Res.67:345-354. Suppl Material (doc)
  53. Zhao, M., F. Wang, S. Liu, K. Xue, Y. Liang, S. Bai, Z. He, J.D. van Nostrand, J.-Z. Zhou, and Y. Yang, B Sun. GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping, Genomics Data, 2:166-169.
  54. Zhao, M., K. Xue, F. Wang, S. Liu, S. Bai, B. Sun, J.-Z. Zhou and Y. Yang. Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping, ISME J. 8(10):2045-2055. Suppl Material (doc)
  55. Zhou, J.-Z., Y. Deng, P. Zhang, K. Xue, Y. Liang, J. D. Van Nostrand, Y. Yang, Z. He, L. Wu, D. A. Stahl, T. C. Hazen, J. M Tiedje, and A. P. Arkin. 2014. Stochasticity, Succession and Environmental Perturbations in a Fluidic Ecosystem. Proc. Nat. Acad. Sci. USA, 111: E836-E845,  doi:10.1073/pnas.1324044111 (Selected as an Editors’ Pick, (Also Editor picks by Genomeweb). Suppl Material (pdf)
  56. Zimmerman, N., J. Izard, C. Klatt, and J.-Z. Zhou and E. Aronson. 2014. The Unseen World: environmental microbial sequencing and identification methods for ecologistsFront Ecol Environ, 12: 224-231. Supplementary Information (pdf)
  1. Bai, S. J. Li, Z. He, J.D. van Nostrand, Y. Tian, G. Lin, J.-Z. Zhou and T. Zheng. 2013. GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Appl. Microbiol. Biotech. 97: 7035-7048. Supplementary Information (doc).
  2. Bartley, L.E., M. L. Peck, S. R. Kim, B. Ebert, C. Manisseri, D. M. Chiniquy, R. Sykes, L. Gao, C. Rautengarten, M. E. Vega-Sánchez, P. I. Benke, P. E. Canlas, P. Cao, S. Brewer, F. Lin, W. L. Smith, X. Zhang, R. E. Jentoff, S. B. Foster, J.-Z. Zhou, A. Ziebell, G. An, H. V. Scheller, P. C. Ronald. 2013. Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification. Plant Physiology, 161: 1615-1633. Suppl Material: Table S1 (xls), Tables (pdf), Figures (pdf)
  3. Chan, Y., J. D. Van Nostrand3, J.-Z. Zhou, S. B. Pointing, and R. L. Farrell. 2013. Functional ecology of an Antarctic Dry Valleys landscape. Proc. Nat. Acad. Sci, 110: 8990-8995. doi: 10.1073/pnas.1300643110. Supplementary Data: Microarray data (xls)Suppl Material (pdf)
  4. Deng Y., Yang Y., He Z., Zhou J. 2013. Molecular ecological network of microbial communities. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference ( Springer-Verlag Berlin Heidelberg, 2013. 2013-03-06 15:51:49 UTC
  5. Eisenlord, S., Z. Freedman, D. Zak, K. Xue, Z. He, and J.-Z Zhou. 2013. Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Appl. Environ. Microbiol., 79: 1191-1199. Suppl Material (pdf)
  6. Freedman, Z., S. D. Eisenlord, K. Xue, D. R. Zak, and J.-Z. Zhou. 2013. Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil Biol. Biochem., 66:130-138. Suppl Material (pdf)
  7. He Z., Van Nostrand J., Zhou J. 2013. GeoChip-based metagenomics technologies for analyzing microbial community functional structure and activities. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference ( Springer-Verlag Berlin Heidelberg, 2013. 2013-03-06 15:48:27 UTC
  8. He, Z., J. Xiong, A. D. Kent, G. Wang, L. Wu, J. D. Van Nostrand, and J.-Z. Zhou. 2013. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem. ISME J, 8: 714-726, doi:10.1038/ismej.2013.177. Suppl Material (pdf)
  9. Jiang, H. Q. He, Z. He, C. L. Hemme, L. Wu, and J.-Z. Zhou. 2013. Continuous Cellulosic Bioethanol Fermentation by Cyclic Fed-Batch Co-Cultivation. Appl. Environ. Microbiol., 79: 1580-1589. Suppl Material (pdf)
  10. Kang*, S.K., J. Van Nostrand*, H. Gough, Z. He, T. C. Hazen, D.A. Stahl, and J.-Z. Zhou. 2013. Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments. FEMS Microbiology Ecology, 86: 200-214.*Authors contributed equally to this work. Supplementary Data: Microarray data (xlsx); Suppl Material: Tables (xls), Figures (pdf), Info (doc)
  11. Lee, Y.-J., J. D. van Nostrand, Q. Tu, Z. Lu, L. Cheng, T. Yuan, Y. Deng, M. Q. Carter, Z. He, L. Wu, F. Yang, J. Xu, and J.-Z. Zhou. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J., 7: 1974-84, doi: 10.1038/ismej.2013.88. Suppl Material: Info (pdf), Figures (pdf)
  12. Li, D., C. Schadel, R., M.L. Haddix, E.A. Paul, R. Conant, J.W. Li, J.Z. Zhou, and Y.Q. Luo. 2013. Differential responses of soil organic carbon fractions to warming: Results from an analysis with data assimilation. Soil Biol. & BioChem., 67: 24-30. Suppl Material (pdf)
  13. Li, D., X. Zhou, L. Wu, J.-Z. Zhou, and Y. Luo. 2013. Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie. Glob Change Biol, 19;3553–3564, doi:10.1111/gcb.12273. Suppl Material (docx)
  14. Li, M.; J. Mathieu, Y. Yang, Yu; S. Fiorenza, Y. Deng, Z. He, J.-Z. Zhou, P. Alvarez. 2013. Widespread distribution of soluble di-iron monooxygenase (SDIMO) genes in Arctic groundwater impacted by 1,4-dioxane. Environ. Sci & Technol., 47:9950-9958. Suppl Material (pdf)
  15. Li, X.Y., Y. Deng, Q. Li, C. Lu, J. Wang, H.W. Zhang, J.G Zhu, J.-Z. Zhou, and Zhili He. 2013. Shifts of functional gene representation in rhizosphere microbial communities under elevated ozone. The ISME J, 7: 660-71. Suppl Material (pdf)
  16. Lin, L, Y. Ji, Q. Tu, R. Huang, L.Teng, X. Zeng, H. Song, K. Wang, Q. Zhou, Y. Li, Q. Qiu, Z. He, J.-Z. Zhou, J. Xu. 2013. Microevolution from Shock to Adaptation Revealed Strategies Improving Ethanol Tolerance and Production in Thermoanaerobacter. Biotechnol Biofuels, 6:103 doi:10.1186/1754-6834-6-103. Suppl Material: Figures (pdf), Tables 1 (xls), 2 (xls), 3 (xls), 4 (xls) 
  17. Penton, C.R., D. St. Louis, Y. Luo, J. Cole, L. Wu, J.-Z. Zhou, T. Schuur, J.-M. Tiedje. 2013. Fungal diversity in permafrost and tallgrass prairie soils under experimental warming. Appl. Environ. Microbiol., 79: 7063-7072. Suppl Material (pdf)
  18. Qiu, D., H. Wei, Q. Tu, Y. Yang, M. Xie, J. Chen, M. H. Pinkerton, Y. Liang, Z. He, and J.-Z. Zhou. 2013. Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1. Appl. Environ. Microbiol., 79: 5250-5257. Suppl Material (pdf)
  19. Siering, P.L., G. V. Wolfe, M. S. Wilson, A. N. Yip, C. M. Carey, C. D. Wardman, R. S. Shapiro, K. M. Stedman, J. Kyle, T. Yuan, J. D. Van Nostrand, Z. He, and J.-Z. Zhou. 2013. Microbial biogeochemistry of boiling springs lake: a physically dynamic, oligotrophic, low pH geothermal ecosystem. Geomicrobiology, 11: 356-376. Suppl Material: Figures (pdf), Videos (link)
  20. Somenahally, A.C., J. J. Mosher, T. Yuan, M. Podar, T. J. Phelps, S. D. Brown, Z. K. Yang, T. C. Hazen, A. P. Arkin, A. V. Palumbo, J. D. Van Nostrand, J.-Z. Zhou, and D. A. Elias. 2013. Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. PLoS One, 8: 8(12): e83909 DOI: 10.1371/journal.pone.0083909. Suppl Material (docx)
  21. Sul, W. J., S. Asuming-Brempong, Q. Wang, D. M. Tourlousse, C. R. Penton, Y. Deng, J. L. M. Rodrigues, S. G.K. Adiku, J. W. Jones, J.-Z. Zhou, J. R. Cole, and J. M. Tiedje. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol. & Biochem., 65:33-38. Suppl Material (docx)
  22. Tu Q, Z. He, Y. Deng, and J.-Z. Zhou. 2013. Strain/species-specific probe design for microbial identification microarrays. Appl Environ Microbiol. 79: 5085-5088. Suppl Material: Table 1 (xls), Table 2 (xls)
  23. Van Nostrand, J. D, T. J. Gentry, and J.-Z. Zhou. 2013. Microarray-Based Microbial Identification and Characterization. In Y.-W. Tang and C. W. Stratton (eds) Advanced Techniques in Diagnostic Microbiology, 2nd ed., Springer, New York, NY (Invited).
  24. Wakelin, S.A., B.I.P. Barratt, E. Gerard; A. L. Gregg, E. L. Brodie, G. L. Andersen, T. Z. DeSantis, J.-Z. Zhou, Z.H. He, G. A. Kowalchuk, M. O’Callaghan. 2013. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology & Biochemistry, 57:675-682. DOI:10.1016/j.soilbio.2012.07.003. Suppl Material: Figures (pdf), Table 1 (xls), Table 2 (xls)
  25. Xu, C., R. Huang, L. Teng, D. Wang, C. L. Hemme, I. Borovok, Q. He, R.l Lamed, E. A. Bayer, J.-Z. Zhou, and J. Xu. 2013. Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. Biotechnology for Biofuels. 6:73 DOI: 10.1186/1754-6834-6-73. Suppl Material: Figures (pdf), Tables 1 (xls), 2 (xls), 3 (xls), 4 (xls) 
  26. Xu, M., Z. He, Y. Deng, L. Wu, J.D. van Nostrand, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2013. Elevated CO2 influences microbial carbon and nitrogen cycling. BMC Microbiology, 13:124. DOI: 10.1186/1471-2180-13-124. Suppl Material (pdf)
  27. Xu M, Y. Fang, J. Liu, X. Chen, G. Sun, J. Guo, Z. Hua, Q. Tu, L. Wu, J.-Z. Zhou, X. Liu. 2013. Draft genome sequence of Shewanella decolorationis S12, adye-degrading bacterium isolated from a water treatment plant. Genome Announce. 1(6):e00993-13. doi:10.1128/genomeA.00993-13.
  28. Xue, K. L. Wu, Y. Deng, Z. He, J. Van Nostrand, G. P. Robertson, T. M. Schmidt, and J.-Z. Zhou. 2013. Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands. Appl. Environ. Microbiol., 79:1284-1294. Suppl Material (pdf)
  29. Yang, Y.F., L. W. Wu, Q. Lin, M.Y. Yuan, D.P Xu, H. Yu, Y.G. Hu, J.C. Duan, X.Z. Li, Z.L. He, K. Xue, S.P. Wang, and J.-Z. Zhou. 2013. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland, Glob Change Biol, 19: 637–648. Supplementary Data: GeoChip Data (xls)Suppl Material (docx)
  30. Yang, Y., J. Chen, D. Qiu, and J.-Z. Zhou. 2013. Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction. BMC Microbiol, 13:267. DOI: 10.1186/1471-2180-13-267. Suppl Material (docs)
  31. Yang, Y., M. Xu, Z. He, J. Guo, G. Sun, J.-Z. Zhou. 2013. Microbial electricity generation enhances decabromodiphenyl ether (BDE-209) degradation. PLoS One, 8:e70686. doi: 10.1371/journal.pone.0070686. Suppl Material (docx)
  32. Zhao, F.-J., E. Harris, J. Yan; J. C. Ma, L.Y. Wu, W.J. Liu, S. McGrath, J.-Z. Zhou, Y.G. Zhu. 2013. Arsenic methylation in soils and its relationship with microbial arsM abundance and diversity, and As speciation in rice. Environ. Sci.& Technol., 47: 7147-7154. Suppl Material (pdf)
  33. Zhang Y, J. Xie, M. Liu, Z. Tian, Z. He, J.D. Van Nostrand, L. Ren, J.-Z. Zhou, and M Yang. 2013. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. Water Research. 47:6298-6308. Supplementary Data: Microarray Data (xlsx)Suppl Material (docx)
  34. Zhang, Y., Z. Lu, S. Liu, Y. Yang, Z. Ren, J.-Z. Zhou, D Li, and Z. He. 2013. GeoChip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau. BMC Microbiology. 13:72. DOI: 10.1186/1471-2180-13-720. Suppl Material (pdf)
  35. Zhang, Z., X. Zhao, Y.T. Liang, G.H. Li, and J.-Z. Zhou. 2013. Microbial functional genes reveal selection of microbial community by PAHs in polluted soils. Environmental Chemistry Letters, 11: 11-17.
  36. Zhou, A., Z. He, Y. Qin, Z. Lu, Y. Deng, Q. Tu, C. L. Hemme, J. D. Van Nostrand, L. Wu, T. C. Hazen, A. P. Arkin, and J.-Z. Zhou. 2013. StressChip as a High Throughput Tool for Assessing Microbial Community. Environ Sci Tech., 47:9841-9849. Supplemental Data: StressChip data (xlsx)Suppl Material (pdf)
  37. Zhou, A., E. Baidoo, Z. He, A. Mukhopadhyay, J. K. Baumohl, P. Benke, M. P. Joachimiak, M. Xie, R. Song, A. P. Arkin, T. C. Hazen, J. D Keasling, J. D. Wall, D. A. Stahl, and J.-Z. Zhou. 2013. Characterization of NaCl-tolerance in Desulfovibrio vulagris Hildenborough through experimental evolution. The ISME J., 7: 1790-1802., doi: 10.1038/ismej.2013.60. Suppl Material (docx)
  38. Zhou, J.-Z., Y.H. Jiang, Y. Deng, Z. Shi, B.-Y. Zhou, K. Xue, L. Wu, Z. He, and Y. Yang. 2013. Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities. mBio 4: e00324-13 (doi:10.1128/mBio.00324-13) (selected as an Editors’ Pick). Supplemental Data: R codes (R format) for predicting overlap with 2 replicates and 3 replicates and for predicting sampling effortSuppl Material (pdf)
  39. Zhou, J.-Z., W. Liu, Y. Deng, Y. Jiang, K. Xue, Z. He, J. D. Van Nostrand, L. Wu, Y. Yang, and A. Wang. 2013. Stochastic assembly leads to alternative communities with distinct functions. mBio, 4: e00584-12. Suppl Material: Figures and Tables (pdf), Info (pdf)
  1. Beazley, M. J., R. J. Martinez, S. Rajan, J. Powell, Y. M. Piceno, L. M. Tom, G. L. Andersen, T. C. Hazen, J. D. Van Nostrand, J.-Z. Zhou, B. Mortazavi, and P. A. Sobecky. 2012. Microbial Community Analysis of a Coastal Salt Marsh Impacted by the Deepwater Horizon Oil Spill. PLoS One, 7: e41305 DOI: 10.1371/journal.pone.0041305. Suppl Material (zip)
  2. Carter, M. Q., K. Xue, M. T. Brandl, F.F. Liu, J. W. Louie, L.Y. Wu, and J.-Z. Zhou. 2012. Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation, PLoSOne, 7: e44186 DOI: 10.1371/journal.pone.0044186 Supplementary Data: Microarray Data (xls)Suppl Material (zip)
  3. Clark, M. E., Z. He, A. M. Redding, M.P. Joachimiak, J.D. Keasling, J.-Z. Zhou, A.P. Arkin, A. Mukhopadhyay, and M. W. Fields. 2012. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics, 13:138. Suppl Material (pdf)
  4. Dassa, B., Ilya Borovok, R. Lamed, B. Henrissat, P. Coutinho, C. L. Hemme, Y. Huang, J.-Z. Zhou and E. A. Bayer. 2012. Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics, 13:210. Suppl Material (doc)
  5. Deng, Y., Y. Jiang, Y. Yang, Z. He, F. Luo, and J.-Z. Zhou. 2012. Molecular Ecological Network Analyses. BMC Bioinformatics, 13:113
  6. Deng, Y., Z. He, M. Xu, Y. Qin, J. D. Van Nostrand, L. Wu, B. A. Roe, G. Wiley, S. E. Hobbie, P. B. Reich, and J.-Z, Zhou. 2012. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities. Appl. Environ. Microbiol., 78:2991-2995. Supplemental Data: Fasta files (zip)Suppl Material (pdf)
  7. Ding, G. C., H. Heuer, Z. He, J. Xie, J.-Z. Zhou, K. Smalla. 2012. More functional genes and convergent overall functional patterns detected by GeoChip in phenanthrene spiked soils. FEMS Microbiol. Ecol. 82: 148-156. DOI: 10.1111/j.1574-6941.2012.01413.x
  8. He, Z., Y. Deng, and J.-Z. Zhou. 2012. Development of functional gene microarrays for microbial community analysis. Curr.Opin. Biotechnol., 23: 49-55. Supplementary Information.
  9. He, Z., Y. Piceno, Y. Deng, M. Xu, Z. Lu, T. DeSantis, G. Andersen, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2012. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J, 6: 259-272. Supplementary Information.
  10. He, Z.L., J. D. Van Nostrand, and J.-Z. Zhou. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr.Opin. Biotechnol., 23:460–466
  11. Huang, W., and J.-Z. Zhou. 2012. Editorial Overview: When single cell technology meets omics, the new toolbox of analytical biotechnology is emerging. Curr. Opin. Biotechnol., 23:1
  12. Liang, Y. H. Gao, X. Guo, J. Chen, G. Qiu, Z. He, J.-Z. Zhou, and X. Liu. 2012. Transcriptome analysis of pellicle formation of Shewanella oneidensis. Archives Of Microbiology, 194: 473-482. Suppl Material (pdf)
  13. Liang, Y., J. D. Van Nostrand, L. A. N’Guessan, A. D. Peacock, Y. Deng, P. E. Long, C. T. Resch, L. Wu, Z. He, G. Li, T. C. Hazen, D. R. Lovley, and J.-Z. Zhou. 2012. Microbial Functional Gene Diversity with a Shift of Subsurface Redox Condition during in situ Uranium Reduction. Appl. Environ. Microbiol., 78:2966-2972. Supplemental Data: Microarray data (xls), Suppl Material: Figures (pdf), Tables (pdf)
  14. Liu, W.Z., A. Wang, Aijie, D. Sun, Dan, N. Ren, Nanqi, Y. Zhang, J.-Z. Zhou. 2012. Characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (MEC). J. Biotechnol. 157: 628-632.
  15. Lomax, C., W. Liu, L. Wu, K. Xue, J. Xiong, J.-Z. Zhou, S. P. McGrath, A. A. Meharg, A. J. Miller, and F-J. Zhao. 2012. Methylated arsenic species in plants originate from soil microorganisms. New Phytologist, 193:665-672. Suppl Material (pdf)
  16. Lu, Z.M., Z. He, V. A. Parisi, S. Kang, Y. Deng, J. D. Van Nostrand, J. R. Masoner, I. M. Cozzarelli, J. M. Suflita, and J.-Z. Zhou. 2012. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ. Sci. Technol., 46: 5824-5833 Supplemental Data: Microarray data (xlsx)Suppl Material (pdf)
  17. Lu, Z.-M., Y. Deng, J. D. Van Nostrand, Z. He, J. Voordeckers, A. Zhou, Y.-J. Lee, O. Mason, E. Dubinsky, K. Chavarria, L. Tom, J. Fortney, R. Lamendella, J. K. Jansson, P. D’haeseleer, T. C. Hazen, and J.-Z. Zhou. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J., 6: 451-460. Supplementary Information (doc) (Highlighted by Science for Environment Policy,, the European Commission's environmental news service for policy makers, titled Microbes degrade oil from Deepwater Horizon spill)
  18. Mason, O. U., T. C. Hazen, S. Borglin, P. S. G. Chain, E. A. Dubinsky, J. L. Fortney, J. Han, H.Y N. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L. M. Tom, S. G. Tringe, T. Woyke, J.-Z. Zhou, E. M. Rubin, and J. K. Jansson. 2012. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill. The ISME J., 6: 1715-1727. Suppl Material (pdf)
  19. Rajeev, L., K. Hillesland, G. Zane, A. Zhou, M. Joachimiak, Z. He, J.-Z. Zhou, A. P. Arkin, J. D. Wall, and D.A. Stahl. 2012. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J. Bacteriol., 194: 5783-93.
  20. Reith, F., R., J. Brugger, C. M. Zammit, A. L. Gregg, K. C. Goldfarb, G. L. Andersen, T. Z. DeSantis, Y. M Piceno, E. L. Brodie, Z. Lu, Z. He, J.-.Z. Zhou, and S. A. Wakelin. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. The ISME J. 6: 2107-2118. Suppl Material (link)
  21. Trivedi, P., Z. He, J. D. Van Nostrand, Gene Albrigo, J.-Z. Zhou, and N. Wang. 2012. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J, 6: 363-383. Supplementary Information.
  22. Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2012. Use of functional gene arrays for elucidating in situ biodegradation. New Frontiers in Microbiology, 3:339.
  23. Walker, C.B. A.M. Redding-Johanson, E. E. Baidoo, L. Rajeev, Z. He, E.L, Hendrickson5, M.P. Joachimiak, S. Stolyar, A. P Arkin, J.A. Leigh, J.-Z. Zhou, J.D. Keasling, A. Mukhopadhyay, and D.A. Stahl. 2012. Functional Responses of Methanogenic Archaea to Syntrophic Growth. Th ISME J., 6: 2045–2055. Suppl Material:  Figures (doc), Tables (xls)
  24. Wang, Y., H. Zheng, F. Chen, J. Zeng, S. Chen, J.-Z. Zhou, and Z. Ouyang. 2012. Methane metabolic microbial community in soils of slash pine plantation and Masson pine plantation. Acta Ecologica Sinica, 32:2-7. (Chinese, DOI:10.5846/stxb201103080280)
  25. Wang, H., Z. He, Z.M. Lu, J.-Z. Zhou, J. D. Van Nostrand, X.H. Xu, and Z.J. Zhang. 2012. Genetic linkage of sediment carbon pools and microbial functions in subtropical freshwater wetlands responding to experimental warming. Appl. Environ. Microbiol., 78: 7652-7661. Suppl Material (pdf)
  26. Wawrik, B., M. Mendivelso, V.A. Parisi, J.M. Suflita, I.A. Davidova, C.R. Marks, J.D. Van Nostrand, Y. Liang, J.-Z. Zhou, B.J. Huizinga, D. Strąpoć, and A.V. Callaghan. 2012. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microb. Ecol., 81: 26-42, DOI: 10.1111/j.1574-6941.2011.01272.x. Suppl Material (pdf)
  27. Wawrik, B., W. Boling, J. Van Nostrand, J.P. Xie, J.-Z. Zhou,D. A. Bronk. 2012. Assimilatory Nitrate Utilization by Bacteria on the West Florida Shelf as Determined by Stable Isotope Probing and Functional Microarray Analysis. FEMS Microbiology Ecology, 79:400-411.
  28. Xie, J, L Wu, JD Van Nostrand, Z He, Z Lu, H Yu, J Xiong, X Liu, and J-Z Zhou. 2012. Improvements on environmental DNA extraction and purification procedures for metagenomics analysis. J Cent South Univ. 19:3055-3063.
  29. Xiong J, Z. He, J.D. Van Nostrand, G. Luo, S. Tu, J.-Z. Zhou, and G. Wang. 2012. Assessing the Microbial Community and Functional Genes in a Vertical Soil Profile with Long-Term Arsenic Contamination. PLoS ONE 7(11): e50507. doi:10.1371/journal.pone.0050507. Suppl Material (zip)
  30. Xu, X., S. Niu, R. A. Sherry, X. Zhou, J.-Z. Zhou, Y. Luo. 2012. Interannual variability in responses of belowground NPP and NPP partitioning to long-term warming and clipping in a tallgrass prairie. Global Change Biology, 18:1648-1656.
  31. Xu, X., Y. Luo, J.-Z. Zhou. 2012. Carbon Quality And The Temperature Sensitivity Of Soil Organic Carbon Decomposition In A Tallgrass Prairie. Soil Biol. & Biochem, 50: 142-148.
  32. Xu, X. R. A. Sherry, S. Niu, J.-Z. Zhou, Yiqi Luo. 2012. Long-term experimental warming decreased labile soil organic carbon in a tallgrass prairie. Plant and Soil, 50: 142-148. DOI: 10.1007/s11104-012-1265-9
  33. Yergeau, E., S. Bokhorst, S. Kang, J.-Z. Zhou, C. W. Greer, R. Aerts, G. A. Kowalchuk. 2012. Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J, 6: 692-702. Supplementary Information (doc)
  34. Zhou, A.F., Y.I. Chen, G. M. Zane, Z.H. He, C. L. Hemme, M. P. Joachimiak, J. Baumohl, Q. He, M. W. Fields, A. P. Arkin, J. D. Wall, T. C. Hazen, and J.-Z. Zhou. 2012. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol., 78:1168-1177. Suppl Material (doc)
  35. Zhou, J.-Z., K. Xue, J.-P. Xie, Y. Deng, L.Y. Wu, X.L. Cheng, S.F. Fei, S.P. Deng, Z.-H. He, J.D. van Nostrand, and Y.Q. Luo. 2012. Microbial Mediation of Carbon Cycle Feedbacks to Climate Warming. Nature Climate Change, 2:106-110. (Ranked by Faculty 1000 as the top 2% of the published articles in biology and medicine). Supplemental Information (pdf)
  1. He, Q., C. L. Hemme, H. Jiang, Z. He, and J.-Z. Zhou. 2011. Mechanisms of Enhanced Cellulosic Bioethanol Fermentation by Co-Cultivation of Clostridium and Thermoanaerobacter spp. BioResource Tech, 102: 9586-9592
  2. He, Z., J. D. Van Nostrand, Y. Deng, and J.-Z. Zhou. 2011. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front. Environ. Sci. Engin. 5: 1-20.
  3. Hemme, C. L., M. W. Fields, Q. He, Y. Deng, L. Lin, Q. Tu, H. Mouttaki, A. Zhou, X. Feng, Z. Zuo, B.D. Ramsey, Z. He, L. Wu, J. Van D. Nostrand, J. Xu, Y. Tang, J. Wiegel, T. J. Phelps, and J.-Z. Zhou. 2011. Correlation of genomic and physiological traits to biofuel yields in Thermoanaerobacter species. Appl. Environ. Microbial., 77: 7998–8008. Suppl Material (doc)
  4. Li, B., W.G. Cao, J.-Z. Zhou, and F. Luo. 2011. Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions. BMC Systems Biology 5:73. Suppl Material (pdf)
  5. Liang, Y.T. J. D. Van Nostrand, Y. Deng, Z. He, L.Y. Wu, X. Zhang, G.H. Li and J.-Z. Zhou. 2011. Functional gene diversity of soil microbial communities from oil-contaminated fields in China. ISME J. 5: 403-413. Suppl Material: Figures (ppt), Tables (doc), Information (oc)
  6. Lin, L., H. Song, Q. Tu, Y. Qin, A. Zhou, W. Liu, Z. He, J.-Z. Zhou, and J. Xu. 2011. The thermoanaerobic Glycobiome Reveals Mechanisms of Pentose and Hexose Co-utilization in Bacteria. PLoS Genetics, 7(10): e1002318. doi:10.1371/journal.pgen.1002318. Suppl Material (zip)
  7. Liu, A.H., L. Wu, Z.L. He, and J.-Z. Zhou. 2011. Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection. Anal Bioanal Chem, 401:2003–2011. Suppl Material (pdf)
  8. Sundararajan, A., J. Kurowski, T. Yan, D. M. Klingman, M.P. Joachimiak, J.-Z. Zhou, B. Naranjo, J. A. Gralnick, and M. W. Fields. 2011. A Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth. Appl. Environ. Microbiol. 77: 4647-4656, doi:10.1128/AEM.03003-10).
  9. Van Nostrand, J.D., Z. He and J. Zhou. 2011. Dynamics of Microbes in the Natural Setting: Development of the GeoChip.  in Environmental Microbiology: Current Technology and Water Applications (Edited by: Keya Sen and Nicholas J. Ashbolt). Caister Academic Press, U.K.
  10. Van Nostrand, J.D., Z. He, J.-Z. Zhou. 2011. GeoChip: A high throughput metagenomics technology for dissecting microbial community functional structure. In: F.J. de Bruijn (ed) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. John Wiley & Sons, New Jersey, pp 509-520.
  11. Van Nostrand, J.D., Z. He, and J.-Z. Zhou. 2011. New developments and applications of microarrays for microbial community analysis in natural and impacted ecosystems. In: M. Moo-Young (ed) Comprehensive Biotechnology, 2e. Elsevier, Amsterdam, The Netherlands.
  12. Van Nostrand, J.D., Z.L. He, and J.-Z. Zhou. 2011. Metagenomics analysis of below-ground microbial communities using microarrays. In: D. Marco (ed) Metagenomics: Current Innovations and Future Trends, Caister Academic. pp 265-288.
  13. Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2011. Microarray analysis of environmental samples. In: Environmental Microbiology: Current Technology and Water Applications. Horizon Scientific, Norwich, UK.
  14. Van Nostrand, J. D., S. Kang, Y. Deng, Y. Liang, Z. He, and J.-Z. Zhou. 2011. Monitoring Microbial Activity with GeoChip. In: J.F. Stolz and R.S. Oremland (eds) Microbial Metal and Metalloid Metabolism: Advances and Applications. ASM Press, Washington DC.
  15. Van Nostrand*, J.D., L.Y. Wu*, W.-M. Wu, Z.J. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carroll, Z. He, B.H. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J.M. Tiedje, T. C. Hazen, and J.-Z. Zhou. 2011. Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer. Appl. Environ. Microbiol, 77:3860-3869 (*Equal distribution). Supplementary Data: Microarray Data (xlsx); Suppl Material: Table (xls), Figures (doc)
  16. Van Nostrand, J.D., and J.-Z. Zhou. 2011. Application of GeoChips in monitoring Carbon cycling. In: N. Jiao, F. Azam, and S. Sander (eds) Microbial Carbon Pump in the Ocean (booklet). AAAS. pp 64-65.
  17. Wang, J., J. D. Van Nostrand, L. Wu, Z. He, G. Li, and J.-Z. Zhou. 2011. Microarray-Based Evaluation of Whole-Community Genome DNA Amplification Methods. Appl. Environ. Microbiol. 77: 4241-4245, (doi:10.1128/AEM.01834-10). Supplementary Information.
  18. Wang, A.J., L.F. Gao, N.Q. Ren, J.F. Xu, C. Liu, G.-L Cao, H. Yu, W.Z. Liu, C. L. Hemme, Z. He, and J.-Z. Zhou. 2011. Isolation and characterization of Shigella flexneri G3 for effective cellulosic saccharification under mesophilic conditions. Appl. Environ. Microbiol. 77: 517-523. Supplementary Information (doc)
  19. Wu, WM, J. Carley, D. Watson , B.H. Gu, S. Brooks, S. S. Kelly, K. Kemner, J. D. van Nostrand , L. Wu, M. Xu, J.-Z. Zhou, J. Luo, E. Cardenas, C. Hwang, M. W. Fields, T. L. Marsh, J. M. Tiedje, S. J. Green, J. E. Kostka, P. K. Kitanidis, P. M. Jardine, C. S. Criddle. 2011. Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Acta Scientiae Circumstaniae. 3: 449-459. (Chinese)
  20. Xie, J.P., H.C., Jiang, X.X. Liu, X.D. Liu, J.-Z. Zhou, and G. Z. Qiu. 2011. 16s rDNA based microbial diversity analysis of eleven acid mine drainages obtained from three Chinese copper mines. Journal of Central South University of Technology, 18: 1930-1939.
  21. Xie, J.P. Z. He, X.X. Liu, X.D. Liu, J. D. Van Nostrand, Y. Deng, L.Y. Wu, J.-Z. Zhou, and G.-Z. Qiu. 2011. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl. Environ. Microbiol. 77: 991-999. Suppl Material (doc)
  22. Zhou, J.-Z.*, Y. Deng*, F. Luo, Z. He, and Y.F. Yang. 2011. Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2. mBio, 2(4): doi:10.1128/mBio.00122-11. (*Equal contribution). Supplementary Data:  Fasta Files (zip), OTU distribution (xlsx)Perl script (zip), Module Eigenvalues Analyses (pdf)Suppl Figures (pdf)
  23. Zhou, J., Q. He, C. L. Hemme, A. Mukhopadhyay, K. Hillesland, A. Zhou, Z. He, J. D. Van Nostrand, T. C. Hazen, D. A. Stahl, J. D. Wall, and A. P. Arkin. 2011. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nature Review in Microbiology. 9:452-466. Supplementary Information (pdf)
  24. Zhou, J-.Z. *, L.-Y. Wu*, Y. Deng, X.-Y. Zhi, Y.-H. Jiang, Q.-C. Tu, J.-P. Xie, J. D. Van Nostrand, Z.-H. He, and Y.-F. Yang. 2011. Reproducibility and Quantitation of Amplicon Sequencing-Based Detection. ISME J. 5:1303-1313, *Equal distribution). Supplementary Data: Fasta files (zip) Suppl Material (link)
  1. Andersen, G. L., Z. He, T.Z. DeSantis, E. L. Brodie, J.-Z. Zhou. 2010. The Use of Microarrays in Microbial Ecology. In: Environmental Molecular Microbiology (Liu, WT; Jansson, JK, eds), pp. 87-109, Caister Academic Press, Wymondham, UK.
  2. Cardenas, E., W.-M. Wu, M. B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P. K. Kitanidis, P. M. Jardine, J.-Z. Zhou, C. S. Criddle, T. L. Marsh, and J. M. Tiedje. 2010. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach. Appl. Environ. Microbiol. 76: 6778-6786. Suppl Material: Legends (pdf); Table S1 (xls); Fig S1 (tif)
  3. Epelde, L., J. M. Becerril, G. A. Kowalchuk, Y. Deng, J.-Z. Zhou, and C. Garbisu. 2010. Impact of metal pollution and thlaspi caerulescens phytoextraction on soil microbial communities. Appl. Environ. Microbiol. 76: 7843-7853.
  4. Gao, H., X. Wang, Z.K. Yang, J. Chen, Y. Liang, H. Chen, T. Palzkill, and J.-Z. Zhou. 2010. Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS ONE, e15295 (DOI:10.1371/journal.pone.0015295). Suppl Material (zip)
  5. Gao, H., S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K. H. Nealson, J. K. Fredrickson, J. M. Tiedje, M. Romine4 and J.-Z. Zhou. 2010. Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microb. Biotech. 3(4): 455-466. Suppl Material: Tables S1 and S2 (doc); Table S3 (xls)
  6. Gao, W.M., T. J.Gentry, T. L. Mehlhorn, S. L. Carroll, P. M. Jardine, and J.-Z. Zhou. 2010. Characterization of Co(III) EDTA reducing bacteria in metal- and radionuclide-contaminated groundwater. Geomicrobiol. J., 27: 93-100.
  7. Gihring, T.M., C.W. Schadt, G.-L. Zhang, Z. Yang, S. Carroll, K. Lowe, T.-L. Mehlhorn, P. Jardine, D. Watson, S.C. Brooks, W. Wu, J.E. Kostka, W. Overholt, S.J. Green, J.-Z. Zhou, P. Zhang, J. D. Van Nostrand. 2010. Changes in microbial community structure and activity during amendment with long-term electron donor sources for bioreduction of groundwater contaminants. Geochimica et Cosmochimica Acta. 74: A329-A329. Suppl Material (pdf)
  8. Hazen, T. C., E. Dubinsky, T. DeSantis, G. Andersen, Y. Piceno, N. Singh, J. Jansson, A. Probst, S. Borglin, J. Fortney, W. Stringfellow, M. Bill, M. Conrad, L. Tom, K. Chavarria, T. Alusi, R. Lamendella, D. Joyner, C. Spier, J. Baelum, M. Auer, M. Zemla, R. Chakraborty, E. Sonnenthal, P. D'haeseleer, H.-Y. Holman, S. Osman, Z.M. Lu, J. van Nostrand, Y. Deng, J.Z. Zhou, and O. U. Mason. 2010. Deep-sea oil plume enriches Indigenous oil-degrading bacteria. Science 330: 204-208. Suppl Information.
  9. He, Q., Z. He, D. C. Joyner, M. Joachimiak, M. N. Price, Z. K. Yang, H.-C. B. Yen, C. L. Hemme, R. Chakraborty, W. Chen, M. M. Fields, D. A. Stahl, J. D. Keasling, M. Keller, A. P. Arkin, T. C. Hazen, J. D. Wall, and J.-Z. Zhou. 2010. Impact of elevated nitrate on sulfate-reducing bacteria: Implications of inhibitory mechanisms in addition to osmotic stress. ISME J. 4: 1386-1397. Suppl Material (link)
  10. He, Z., Y. Deng, J. D. Van Nostrand, Q. Tu, M. Xu, C. Hemme, X. Li, L. Wu, T. J. Gentry, Y.F. Yin, J. Liebich, T. C. Hazen, and J-Z. Zhou. 2010. GeoChip 3.0 as a high throughput tool for analyzing microbial community structure, composition, and functional activity. ISME J. 4: 1167-1179. Supplementary Information (doc)
  11. He, Z., M. Xu, D. Ye, S. Kang, L. Kellogg, L.Y. Wu, J. D. Van Nostrand, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol. Lett. 13: 564-575 (Highlighted by Science as an example of the frontier of integrative biodiversity studies, Naeem et al. 2012. Science: 336: 1401-1406). Supplementary Information (doc)
  12. He, Z., A.F. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, K. Huang, E. J. Alm, M. W. Fields, J. Wall, D. Stahl, T. C. Hazen, J. D. Keasling, A. P. Arkin, and J.-Z. Zhou. 2010. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl. Environ. Microbiol. 76:1574-1586. Supplementary Information.
  13. Hemme, C. L., H. Mouttaki, Y.-J. Lee, L. Goodwin, S. Lucas, A. Copeland, A. Lapidus, T. G. d. Rio, H. Tice, E. Saunders, T. Brettin, J. C. Detter, C. S. Han, S. Pitluck, M. L. Land, L. J. Hauser, N. Krypides, N. Mikhailova, Z. He, L. Wu, J. D. V. Nostrand, B. Henrissat, Q. He, P. A. Lawson, R. S. Tanner, L. R. Lynd, J. Wiegel, M. W. Fields, A. P. Arkin, C. W. Schadt, B. S. Stevenson, M. J. McInerney, Y. Yang, H. Dong, Denfeng Xing, Nanqi Ren, Aijie Wang, R. L. Huhnke, J. R. Mielenz, S.-Y. Ding, M. E. Himmel, S. Taghavi, D. v. d. Lelie, E. M. Rubin, and J.-Z. Zhou. 2010. Sequencing of Multiple Clostridia Genomes Related to Biomass Conversion and Biofuels Production. Journal of Bacteriology, 192: 6494-6496.
  14. Hemme, C. L., Y. Deng, T. J. Gentry, M. W. Fields, L. Wu, Z. Fang, S. Barua, K. Barry, S. Green-Tringe, D. B. Watson, Z. He, T. C. Hazen, J. M. Tiedje, E. M. Rubin and J.-Z Zhou. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J.5: 660-672. (Highlighted by The Scientist, Supplementary Information.
  15. Huang, Y., W.M. Zong, X. Yan, R.F. Wang, C.L. Hemme, J.-Z. Zhou, Z.H. Zhou. 2010. Succession of the Bacterial Community and Dynamics of Hydrogen Producers in a Hydrogen-Producing Bioreactor. Appl. Environ. Microbiol. 76: 3387-3390. Supplementary Information (doc)
  16. Kimes, N. E., J. D.Van Nostrand, E.Weil, J.-Z. Zhou, and P.J. Morris. 2010. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ. Microbiol. 12: 541-556.
  17. Liang, Y., H. Gao, J. Chen, Y. Dong, L. Wu, Z. He, X. Liu, G. Qiu, and J.-Z. Zhou. 2010. Pellicle formation in Shewanella oneidensis. BMC Microbiol. 10: 291 (DOI: 10.1186/1471-2180-10-291). Suppl Material (pdf)
  18. Liang. Y.T., Z. He, L. Y. Wu, Y. Deng, G.H. Li, and J.-Z. Zhou. 2010. Development of a common oligo reference standard (CORS) for microarray data normalization and comparison across different microbial communities. Appl. Environ. Microbiol. 76: 1088-1094.
  19. Lin L., H.H. Song, Y.T. Ji, Z. He, Y.T. Pu, J.-Z. Zhou, and J. Xu. 2010. Ultrasound-mediated DNA transformation in thermophilic Gram-positive anaerobes. PLoS One 5(9): e12582 (doi:10.1371/journal.pone.0012582). Suppl Material (zip)
  20. Liu, W.Z., A.J. Wang, S. Cheng, B. E. Logan, H. Yu, Y. Deng, J. D. van Nostrand, L.Y. Wu, Z. He and J.-Z. Zhou. 2010. GeoChip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environ. Sci. Technol. 44: 7729-7735. Supplementary Information.
  21. Mason, O. U., T. Nakagawa, M. Rosner, J. D. Van Nostrand, J.-Z. Zhou, A. Maruyama, M. R. Fisk, S. J. Giovannoni. 2010. First Investigation of the Microbiology of the Deepest Layer of Ocean Crust. PLoS ONE 5(11): e15399 (doi:10.1371/journal.pone.0015399). Suppl Material (zip)
  22. Parnell, J. J., G. Rompato, L. C. Latta IV, M. E. Pfrender, D. Naftz, J. VanNostrand, Z. He, J.-Z. Zhou, G. Andersen, P. Champine, B. Ganesan, and B. C. Weimer. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoS ONE 5: e12919 (doi:10.1371/journal.pone.0012919). Suppl Material (zip)
  23. Reeve, J., C. W. Schadt, L. Carpenter-Boggs, S.H. Kang, J.-Z. Zhou, and J. P. Reganold. 2010. Effects of soil type and farm management on soil ecological functional genes and microbial activities. ISME J. 4: 1099-1107. Suppl Material (link)
  24. Reganold, J.P., P.K. Andrews, J.R. Reeve, L. Carpenter-Boggs, C.W. Schadt, J.R. Alldredge, C.F. Ross, N.M. Davies, and J.-Z. Zhou. 2010. Fruit and soil quality of organic and conventional strawberry agroecosystems. PLoS ONE 5: e12346 (doi:10.1371/journal.pone.0012346). Suppl Material (zip)
  25. Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2010. Analysis of microbial communities by functional gene arrays. In: L. Barton, M. Mandl and A. Loy (eds) Geomicrobiology: Molecular and Environmental Perspective. Springer, New York. Pp 109-126.
  26. Van Nostrand, J. D, Y. Liang, Z. He, G. Li, and J.-Z. Zhou. 2010. GeoChip: A high throughput genomic tool for linking community structure to functions. In: K. N. Timmis (ed) Handbook of Hydrocarbon and Lipid Microbiology, vol 4, Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids. Springer, New York, pp 2677-2685.
  27. Van Nostrand, J. D, L. Wu, Z. He, and J.-Z. Zhou. 2010. GeoChips for analysis of microbial functional communities. In: J. R. van der Meer (ed) Handbook of Hydrocarbon and Lipid Microbiology, vol 5, Experimental Protocols and Appendices. Springer, New York, pp 4039-4050.
  28. Wang, A.J., W.Z., Liu WZ, N. Q. Ren, J.-Z. Zhou, and A.A. Cheng. 2010. Key factors affecting microbial anode potential in a microbial electrolysis cell for H2 production. International Journal of Hydrogen Energy 35: 13481-13487.
  29. Wu, M.-M., J. Carley, S. J. Green, J. Luo, S. D. Kelly, J. D. van Nostrand, K. Lowe, T. Mehlhorn, S. Carroll, B. Boonchayanant, F.E. Löfller, D. Watson, K.M. Kemner, J.-Z. Zhou, P. K. Kitanidis, J. E. Kostka, P. M. Jardine, and C. S. Criddle. 2010. Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface. Environ. Sci. Technol. 44: 5104-5111. Supplementary Information (pdf)
  30. Wu, WM, J. Carley, D. Watson, B.H. Gu, S. Brooks, S. S. Kelly, K. Kemner, J. D. Van Nostrand, L. Wu, M. Xu, J.-Z. Zhou, J. Luo, E. Cardenas, C. Hwang, M. W. Fields, T. L. Marsh, J. M. Tiedje, S. J. Green, J. E. Kostka, P. K. Kitanidis, P. M. Jardine, C. S. Criddle. 2010. Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Acta Scientiae Circumstaniae. 31:449-459. (Chinese)
  31. Xiong, J.B., L.Y. Wu, S.X. Tu, J. D. van Nostrand, Z. He, J.-Z. Zhou, and G.J. Wang. 2010. Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the rhizosphere of the arsenic hyper-accumulating plant Pteris vittata L. Appl. Environ. Microbiol 76: 7277-7284. Suppl Material (pdf)
  32. Xu, M.Y., W.-M. Wu, L.Y. Wu, Z. He, J.D. Van Nostrand, Y. Deng, J. Luo, J. Carley, M. A. Ginder-Vogl, T. Gentry, B. Gu, D. Watson, P. M. Jardine, C. S. Criddle, and J.-Z. Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J. 4: 1060-1070. Supplementary Information (doc)
  33. Yang, Y., L. A. McCue, A. B. Parsons, C. X. Guan, S. Feng and J.-Z. Zhou. 2010. The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control. BMC Microbiology 10:264 (DOI: 10.1186/1471-2180-10-264).
  34. Zhou, A.-F, Z. He, A. M. Redding, A. Mukhopadhyay, C. L. Hemme, M. P. Joachimiak, K. S. Bender, J. D. Keasling, D. A. Stahl, M. W Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J.-Z. Zhou. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ. Microbiol. 12: 2645-2657. Suppl Material
  35. Zhou*, J.-Z., Y. Deng*, F. Luo, Z.-H. He, Q. Tu, and X.Y. Zhi. 2010. Functional Molecular Ecological Networks. mBio 1(4):e00169-10 (doi:10.1128/mBio.00169-10, *equal contribution). Suppl Material: Tables (doc), Figures (pdf)
  36. Zhou, J.-Z., Z. He, J. D. Van Nostrand, L.Y. Wu, and Y. Deng. 2010. Applying GeoChip Analysis to Disparate Microbial Communities. Microbe, 5:60-64.
  1. Feng, X.Y., H. Mouttaki, L. Lin, R. Huang, B. Wu, C. L. Hemme, Z. He, B. Zhang, L. Hicks, J. Xu, J.-Z. Zhou, and Y. J. Tang. 2009. Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp. X514 via Isotopomer-Assisted Metabolite Analysis. Appl. Environ. Microbiol. 75: 5001-5008. Supplemental Information (doc)
  2. Gao, H., Z.K Yang, S. Barua, S. B. Reed, M. F. Romine, K. H. Nealson, J. K. Fredrickson, J. M. Tiedje, and J.-Z. Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. ISME J. 3: 966-976. Suppl Material (pdf)
  3. Gentry TJ, He Z and Zhou J. 2009. Detection and characterization of uncultivated microorganisms using microarrays. In Uncultivated Microorganisms (Microbiology Monographs) Vol. 10: 179-202, Epstein, Slava S. (Ed.) Springer-Verlag Berlin Heidelberg (Invited review).
  4. He, Q., P. M. Lokken, and J.-Z. Zhou. 2009. Characterization of the Impact of Acetate and Lactate on Ethanolic Fermentation by Thermoanaerobacter ethanolicus. Bioresource Technology 100: 5955-5965.
  5. Hwang, C., W. Wu, T.J. Gentry, J. Carley, S.L. Carroll, D. Watson, P.M. Jardine, J.-Z Zhou, C.S. Criddle, and M.W. Fields. 2009. Bacterial Community Succession During in situ Uranium Bioremediation: Spatial Similarities Along Controlled Flow Paths. ISME J. 3: 47-64. Suppl Material (pdf)
  6. Liang, Y.L., Z.L. He, H.C. Gao HC, G.Z. Qiu, J.-Z. Zhou, and X.-D. Liu. 2009. Characterization of cytochrome mutants for pellicle formation in Shewanella oneidensis MR-1. Trans. Nonferrous Met. Soc. China 19: 700-706.
  7. Liang, Y.T, G. Li, J. D. Van Nostrand, Z. He, L.Y. Wu, Y. Deng, X. Zhang, and J.-Z. Zhou. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiol. Ecol. 70: 324-333. Suppl. Info.
  8. Liang, Y., J. Wang, J. D. Van Nostrand, J.-Z. Zhou, X. Zhang, G. Li. 2009. Microarray-based functional gene analysis of soil microbial communities in ozonation and biodegradation of crude oil. Chemosphere, 75: 193-199.
  9. Liebich, J. T. Wachtmeister, J.-Z. Zhou, and P. 2009. Degradation of Diffuse Pesticide Contaminants: Screening for Microbial Potential Using a Functional Gene Microarray. Vadose Zone Journal 8: 703-710.
  10. Luo, W.S., S. D. Kelly, K. M. Kemner, D. Watson , J.-Z. Zhou, P.M. Jardine, and B.H. Gu. 2009. Sequestering Uranium and Technetium through Co-Precipitation with Aluminum in a Contaminated Acidic Environment. Environ. Sci. Technol. 43: 7516-7522. Suppl. Info.
  11. Mason, O. U., C. A DiMeo-Savoie, J. D. Van Nostrand, J.-Z. Zhou, M. R. Fisk, and S. J. Giovannoni. 2009. Prokaryotic diversity, distribution, and preliminary insights into their role in biogeochemical cycling in marine basalts. ISME J. 3: 231-242. Suppl. Info.
  12. Ning, J., J. Liebich, M. Kastner, J.-Z Zhou, A. Schaffer, P. and Burauel. 2009. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl. Microbiol. Biotechnol. 82: 983-993
  13. Singh BK, CD Campbell, SJ Sorenson, and J Zhou. 2009. Soil genomics. Nat. Rev Microbiol. 7:756
  14. Tas, N., M. H.A. van Eekert, G. Schraa, J.-Z. Zhou, W. M. de Vos, and H. Smidt. 2009. 2009. Tracking Functional Guilds: Dehalococcoides spp. in European River Basins Contaminated with Hexachlorobenzene. Appl. Environ. Microbiol. 75: 4696-4704. Supplementary Information (doc)
  15. Van Nostrand, J. D, W.-M. Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C. Criddle, P. Jardine, J. M. Tiedje, T. C. Hazen, J.-Z. Zhou. 2009. GeoChip-based analysis of functional microbial communities in a bioreduced uranium-contaminated aquifer during reoxidation by oxygen. Environ. Microbiol. 11: 2611-2626. Supplementary Information (doc)
  16. Waldron, P. J., J. D.Van Nostrand, D. B. Watson, Z. He, L. Wu, P. M. Jardine, T. C. Hazen, and J.-Z. Zhou. 2009. Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels. Environ. Sci. Technol. 43: 3529-3534. Suppl. Info.
  17. Walker, C. B., Z. He, Z. K. Yang, J. A. Ringbauer, Jr., J.-Z. Zhou, G. Voordouw, J. D. Wall, A. P. Arkin, T.C. Hazen, S. Stolyar, and D. A. Stahl. 2009. The Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris. J. Bacteriol. 191: 5793-5801. Suppl Material: Tables (pdf), Figures (pdf)
  18. Walker, C, S. S. Stolyar, D. Chivian, N. Pinel, J. A. Gabster, P. S. Dehal, Z. He, Z. K. Yang, H. B. Yen, J.-Z. Zhou, J. D. Wall, T. C. Hazen, A. P. Arkin, D. A. Stahl. 2009. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environ. Microbiol. 11: 2244-2252. Suppl Material: Tables S1-7 (pdf); Table S6 (pdf), Figures S1 (tif), S2 (tif), S3 (tif), S4 (tif), S5 (tif)
  19. Wang, A.J., W. Z., Liu, S.A. Cheng, D.F. Xing, J.-Z. Zhou, and B. E. Logan. 2009. Source of methane and methods to control its formation in single chamber microbial electrolysis cells. International J Hydrogen Energy 34: 3653-3658.
  20. Wang, F., H. Zhou, J. Meng, X.T. Peng, L. Jiang, P. Sun, C. Zhang, J. D. Van Nostrand , Y. Deng, Z. He, L. Wu, J.-Z. Zhou, X. Xiao. 2009. GeoChip-based Analysis of Metabolic Diversity of Microbial Communities at the Juan de Fuca Ridge Hydrothermal Vent. Proc Nat. Acad. Sci, 106: 4840-4845. Suppl. Info. (pdf)
  21. Yang Y. , D. P. Harris, F. Luo, W. Xiong, M. Joachimiak, L. Wu, P. Dehal. J. Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin, and J.-Z. Zhou. 2009. Snapshot of Iron Response in Shewanella oneidensis by Gene Network Reconstruction. BMC Genomics 10:131. Suppl Material (jpeg)
  22. Zhou, J.-Z., 2009. Predictive Microbial Ecology. Microb. Biotechnol. 2: 154–156
  23.  Brajesh K. Singh, B.K., C. D. Campbell, S. J. Sorenson, and J.-Z. Zhou. 2009. Soil genomics is the way forward. Nat. Rev. Microbiol. 7: 10 (DOI: 10.1038/nrmicro2119-c1).
  1. Cardenas, E., W. Wu, M.B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P. K. Kitanidis, P.M. Jardine, J.-Z.,Zhou, C.S. Criddle, T.L. Marsh and J.M. Tiedje. 2008. Microbial Communities in Contaminated Sediments Associated with Bioremediation of Uranium to Submicromolar Levels. Appl. Environ. Microbiol. 74: 3718-3729.
  2. Deng, Y., Z. He, J. D. Van Nostrand, J.-Z. Zhou. 2008. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics, 9:491 (doi:10.1186/1471-2164-9-491). Supplemental Information (xls)
  3. Gao, H.C., X.H. Wang, Z.K. Yang, T. Palzkill, and J.-Z. Zhou. 2008. Probing Regulon of ArcA in Shewanella oneidensis MR-1 by Integrated Genomic Analyses. BMC Genomics 9: 42. Suppl Material: File 1 (ppt); File 2 (doc); File 3 (doc); File 4 (doc); File 5 (doc)
  4. Gao, H., D. Pattison, T. Yan, D. M. Klingeman, X. Wang, J. Petrosino, L. Hemphill, X. Wan, A.B. Leaphart, G. Weinstock, T. Palzkill, and J.-Z. Zhou. 2008. Generation and Validation of a Shewanella oneidensis MR-1 Clone Set for Protein Expression and Phage Display. PLoS One 3(8): e2983. Supplementary Information (xls).
  5. He, Z., and J.-Z. Zhou. 2008. Empirical determination of signal to noise ratio (SNR) thresholds for microarray analysis. Appl. Environ. Microbiol. 74: 2957–2966. Suppl Material (doc)
  6. He, Z., and J.-Z. Zhou. 2008. Selection of oligonucleotide probes for microarrays. In: Molecular Microbial Ecology Manual 2nd, Springer Netherlands. pp1880-1891. (Invited review).
  7. He, Z, J. D.Van Nostrand, L. Wu, and J.-Z. Zhou. 2008. Development and application of functional gene arrays for microbial community analysis. Trans. Nonferrous Met. Soc. China 18: 1319-1327 (Invited review).
  8. Pereira, P.M. Q. He, A.V. Xavier, J.-Z. Zhou, I.A. C. Pereira and R. O. Louro. 2008. Transcriptional Response of Desulfovibrio vulgaris Hildenborough to Oxidative Stress Mimicking Environmental Conditions. Archives of Microbiology, 189: 451-461. Suppl Material (doc)
  9. Pereira, P. M., Q. He, F. M. A. Valente, A. V. Xavier, J.-Z. Zhou, I. A. C. Pereira & R. O. Louro. 2008. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 93:347-362.
  10. Rodrigues, D. F., N. Ivannova, Z. He, M. Huebner, J.-Z. Zhou and J. M. Tiedje. 2008. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics 9:547 (doi:10.1186/1471-2164-9-547). Supplementary Information (doc)
  11. Wang, X., H. Gao, Y. Shen, G. M. Weinstock, J.-Z. Zhou, and T. Palzkill. 2008. A High-throughput Percentage-of-Binding Strategy to Measure Binding Energies in DNA-Protein Interactions: Application to Genome Scale Site Discovery. Nucleic Acids Res. 36: 4863-4871. Supplementary Information (doc)
  12. Wu, L. Y., X.D. Liu, M.W. Fields, D.K. Thompson, C.E. Bagwell, J.M. Tiedje, T.C. Hazen, and J.-Z. Zhou. 2008. Microarray-based whole-genome hybridization as a tool for determining prokaryotic species relatedness. ISME J. 2, 642–655. Suppl Material (doc)
  13. Wu*, L., L. Kellogg, A.H. Devol, A.V. Palumbo, J.M. Tiedje, and J.-Z. Zhou*. 2008. Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments From the Gulf of Mexico. Appl. Environ. Microbiol. 74: 4516-4529 (*equal contribution). Suppl Material: Table S1 (zip)
  14. Yang, Y.F., D.P. Harris, F. Luo, L.Y. Wu, A.B. Parsons, A. V. Palumbo and J.-Z. Zhou. 2008. Characterization of the Shewanella oneidensis Fur Gene: Roles in Iron and Acid Tolerance Response. BMC Genomics 9(Suppl 1):S11. Suppl Material: Figures S1 (jpg) and S2 (jpg)
  15. Yang, Y., M. Zhu, L. Wu, and J.-Z. Zhou. 2008. Assessment of Data Processing to Improve Reliability of Microarray Experiments Using Genomic DNA Reference. BMC Genomics 9(Suppl 2):S5 (doi:10.1186/1471-2164-9-S2-S5).
  16. Yin, H., G. Qiu, L. Wu, M. Xie, J. Zhou, Z. Dai, D. Wang, L. Kellogg, L. Cao and X. Liu (2008). "Microbial community diversity and changes associated with a mine drainage gradient at the Dexing copper mine, China". Aquatic Microbial Ecology 51:67-76.
  17. Yin, H. Q., L. Cao, G. Qiu, D. Wang, L. Kellogg, J.-Z. Zhou, X. Liu, Z. Dai, J. Ding, X. Liu. 2008. Molecular diversity of 16S rRNA and gyrB genes in copper mines. Archives of Microbiology, 189: 101-110.
  18. Yin, H., L. Cao, M. Xie, Q. Chen, G. Qiu, J.-Z. Zhou, L. Wu, D. Wang, X. Liu. 2008. Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China. Syst. Appl. Microbiol. 31: 302-311.
  19. Zhou, J.-Z*, S. Kang*, C. W. Schadt, and C.T. Garten, Jr. 2008. Spatial Scaling of Functional Gene Diversity across Various Microbial Taxa. Proc. Nat. Acad. Sci, 105: 7768-7773 (*equal contribution). Supplementary Informaiton (pdf)
  1. Amos, B. K., Y. Sung, K. E. Fletcher, T. J. Gentry, J.-Z. Zhou, and F. E. Löffler. 2007. Detection and Quantification of Geobacter lovleyi Strain SZ: Implications for Bioremediation at Tetrachloroethene- (PCE-) and Uranium-Impacted Sites. Appl. Environ. Microbiol. 73: 6898-6904.  Suppl text.
  2. Bender, K.S., H. Yen, C. L. Hemme, Z Yang, Z. He, Q. He, J.-Z. Zhou, K. Huang, E. J. Alm, T. C. Hazen, A. P. Arkin, and J. D. Wall. 2007. Analysis of a Ferric Uptake Regulator (Fur) Mutant of Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol. 73: 5389-5400.
  3. Bretschger, O., A Obraztsova, C. A. Sturm, I. Chang, Y. A. Gorby, S. B. Reed, D. E. Culley, C. L. Reardon, S.Barua, M.F. Romine, J.-Z. Zhou, A.S. Beliaev, R. Bouhenni, D. Saffarini, F. Mansfeld, B.H. Kim, J. K. Fredrickson, and K.H. Nealson. 2007. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl. Environ. Microbiol. 73:7003-7012. Suppl Material: Methods (doc); Fig S1 (doc)
  4. Butler, J. E., Q. He, K. P. Nevin, Z. He, J.-Z. Zhou, D. R. Lovley. 2007. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics 8:180.
  5. Caffrey, S., H. S. Park, J. Voordouw, Z. He, J.-Z. Zhou, and Gerrit Voordouw. 2007. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 89: 6159–6167. Supplementary Information (xls)
  6. Gao, H., Z. K. Yang, T. J. Gentry, L.Wu, C. W. Schadt, and J.-Z. Zhou. 2007. Microarray-based Analysis of Microbial Community RNAs by Whole Community RNA Amplification (WCRA). Appl. Environ. Microbiol. 73: 563-571. (The 8th of the top 20 papers most requested in 2007 (January to March) by AEM).
  7. Garten, C.T., S. Kang, D.J. Brice, C. W. Schadt, and J.-Z. Zhou. 2007. Variability in Soil Properties at Different Spatial Scales (1 m to 1 km) in a Deciduous Forest Ecosystem. Soil Biol. Biochem. 39: 2621-2627.
  8. Gentry,T., C. Schadt, and J.-Z. Zhou. 2007. Functional gene array for microbial community analysis. Pp. 1052-1062. In Hurst, C.J, Crawford, R. L., Mills, A. L., Garland, J.L., Stetzenbach, L. D., and Lipson, D. A. (eds), The 3rd edition of the ASM Manual of Environmental Microbiology, (Invited), ASM Press, Washington DC.
  9. He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, W.M. Wu, B. Gu, P. Jardine, C. Criddle, and J.-Z. Zhou. 2007. GeoChip: A comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. The ISME Journal, 1: 67-77 (News Release by Nature Press Office: ( (One of the top few highly cited in this Journal). Supplementary Information: Suppl1 (doc)Table of all probes (xls)
  10. Huang, Z., C. Zhang, B.P. Hedlund, J. Wiegel, J.-Z. Zhou. 2007. Molecular phylogeny of uncultivated Crenarchaeota in Great Basin hot springs of moderately elevated temperature. Geomicrobiology J. 24: 535-542.
  11. Leigh, M.B., V.H. Pellizari, O. Uhlik, R. Sutka, J. Rodrigues, N. E. Ostrom, J.-Z. Zhou, and J. M. Tiedje, 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J. 1: 134-148.
  12. Luo, F., Y. Yang, C. Chen, J.-Z. Zhou, R. H. Scheuermann. 2007. Modular Organization of Protein Interaction Networks. Bioinformatics. 23: 207-214.
  13. Luo, W., W. Wu, T. Yan, C. S. Criddle, P. M. Jardine, J.-Z. Zhou, and B, Gu. 2007. Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition. Appl.Microbiol. Biotechnol. 77: 713-721.
  14. Luo*, F., D. Yang*, J. Zhong, H. Gao, L. Khan, D. K. Thompson and J.-Z. Zhou. 2007. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics, 8:299 (*Equal contribution). Suppl Material: Figures (pdf); RMT Notes (pdf); Tables (pdf)
  15. Mukhopadhyay A., A.M. Redding, M.P. Joachimiak, A.P. Arkin, S.E. Borglin, P.S. Dehal, R. Chakraborty, J.T. Geller, T.C. Hazen, Q.He, D.C. Joyner, V.J. J. Martin, J.D. Wall, Z. K. Yang, J.-Z. Zhou, and J.D. Keasling. 2007. Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 189:5996-6010. Suppl Material: ITRAQ Data (zip); Figure S1 (zip); Table S1 (zip
  16. Stolyar, S., Q. He, M.P. Joachimiak, Z. He, Z. K. Yang, S. E. Borglin, D.C. Joyner, K. Huang, E. Alm, T. C. Hazen, J.-Z. Zhou, J.D. Wall, A.P. Arkin, and D.A. Stahl. 2007. Response of Desulfovibrio vulgaris to alkaline stress. J. Bacteriol. 189: 8944-8952. Suppl Material: Tables S1 (zip), S2 (zip), S3 (zip); Figure S1 (zip
  17. Van Nostrand, J. D., T.V. Khijniak, T.J. Gentry, M.T. Novak, A.G. Sowder, J.-Z. Zhou, P.M. Bertsch and P.J. Morris. 2007. Isolation and Characterization of Four Gram-Positive Nickel-Tolerant Microorganisms from Contaminated Riparian Sediments. Microb. Ecol. 53: 670-682.
  18. Wagner M., H. Smidt, A. Loy, J.-Z. Zhou. 2007. Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions. Microbial Ecol. 53:498-506
  19. Wu, W., J. Carley, J. Luo, M. A Ginder-Vogel, E. Cardenas, M.B. Leigh, C.C. Hwang, S. D. Kelly, C. Ruan, L.Wu, J. Van Nostrand, T. Gentry , K. Lowe, T. Mehlhorn, S. Carroll, M. W. Fields, B. Gu, D. Watson, K. M. Kemner, T. Marsh, J.M. Tiedje, J.-Z. Zhou, Scott Fendorf, Peter K. Kitanidis, Philip M. Jardine, and Craig S. Criddle. 2007. In Situ Bioreduction of Uranium (VI) to Submicromolar Levels and Reoxidation by Dissolved Oxygen. Environ. Sci. Technol. 41: 5716-5723. Supplementary Information (pdf)
  20. Yang Y., M.Wan, W. Shi, H. Peng, G. Qiu, J.-Z. Zhou, X. Liu. 2007. Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China. Aquatic Microb. Ecol 47: 141-151.
  21. Yergeau, E., S. Kang, Z. He, J.-Z., Zhou, and G. A. Kowalchuk. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J. 1: 163-179. Supplementary Information (pdf)
  22. Yin, H., L. Cao, G. Qiu, D. Wang, L. Kellogg, J.-Z. Zhou, Z. Dai, X. Liu, 2007. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems. J. Microbiol. Methods 70: 165-178.
  23. Zhang, Y., X. Zhang, X. Liu, Y. Xiao, L. Qu, L. Wu, J.-Z. Zhou, 2007. Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. FEMS Microbiol. Lett. 266: 144-151.
  24. Zhou, X., and J.-Z. Zhou. 2007. Antibody-microarrays on hybrid polymeric thin film-coated slides for multiple-protein Immunoassays., In: Rampal, JB (ed), Microarrays: Volume 2: Applications and Data Analysis, Vol. 382, Methods in Molecular Biology, The Humana Press Inc, New Jersey, USA Pp. 257-270. (Invited).
  1. Bagwell, C. E., X. Liu, L. Wu, and J.-Z. Zhou. 2006. Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer. FEMS Microbiol. Ecol. 55:424-431.
  2. Brown, S. D., M. Martin, K. Huang, E. Alm, Y. Yang, A. Arkin, J.-Z. Zhou, and D. K. Thompson. 2006. Cellular Response of Shewanella oneidensis to Strontium Stress. Appl. Environ. Microbiol. 72: 890-900. Supplemental Material.
  3. Brown, S. D., M. R. Thompson, N. C. VerBerkmoes, K. Chourey, M. Shah, J.-Z. Zhou, R. L. Hettich, and D. K. Thompson. 2006. Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress. Molecular and Cellular Proteomics 5: 1054-1071. Suppl Material (link)
  4. Chhabra, S.R., Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T.C. Hazen, J. D. Wall, J.-Z. Zhou, A. P. Arkin, and A.K. Singh. 2006. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 188: 1817-1828. Suppl Material: Table S1 (zip); Table S2 (zip)
  5. Cho, C. M., T. Yan, X. Liu, L. Wu, J.-Z. Zhou, and L.Y. Stein. 2006. Transcriptome of Nitrosomonas europaea with a disrupted nitrite reductase (nirK) gene. Appl. Environ. Microbiol. 70:4450-4454. Supplemental Information (xls)
  6. Chourey, K., M. Thompson, J. Morrell-Falvey, N. C. VerBerkmoes, S. D. Brown, M. Shah, J.-Z. Zhou, M. Doktycz, R. L. Hettich, and D. K. Thompson. 2006. Global molecular and morphological effects of 24-hour chromium (VI) exposure on Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 72: 6331-6344
  7. Clark, M.E., Q. He, Z. He, K. Huang, E.J. Alm, X. Wan, T.C. Hazen, A.P. Arkin, J.D. Wall, J.-Z. Zhou, and M.W. Fields. 2006. Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase growth during electron donor depletion. Appl. Environ. Microbiol. 72: 5578-5588. Supplementary Material.
  8. Fields, M.W., J. Schryver, C. C. Brandt, T. Yan, J.-Z. Zhou, and A.V. Palumbo. 2006. Confidence intervals for similarity values achieved from direct sequence determination of cloned SSU rRNA genes from environmental samples. J. Microbiol. Methods, 65: 144-152.
  9. Fields, M.F., C.E. Bagwell, S.L. Carroll, T. Yan, X. Liu, D.B. Watson, P.M. Jardine, C.S. Criddle, T.C. Hazen, and J.-Z. Zhou. 2006. Phylogenetic and functional biomarkers as indicators of bacterial community responses to mixed-waste contamination. Environ. Sci. Technol. 40: 2601-2607.
  10. Gao, H., Z. K. Yang, L. Wu, D. K. Thompson, and J.-Z. Zhou. 2006. Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. J. Bacteriol. 188:4560-4569. Suppl Material: Figure S1 (doc); Table S1 (doc)
  11. Gao, H., A. Obraztova, N. Stewart, R. Popa, J. K. Fredrickson, J. M. Tiedje, K., H. Nealson, and J.-Z. Zhou. 2006. Shewanella loihica sp. nov., isolated from iron-rich microbial mats in Pacific Ocean. Int. J. Syst. Evol. Microbiol. 56: 1911-1916. Supplementary Material.
  12. Gao, W., Y. Liu, C. S. Giometti, L. Wu, X. Liu, T. Yan, D. Stanek, D. Xu, Y. Xu, M. W. Fields, and J.-Z. Zhou. 2006. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1. BMC Genomics 7:76.
  13. Gentile, M, T. Yan, S. M. Tiquia, M. W. Fields, J. Nyman, J.-Z. Zhou, and C. S. Criddle. 2006. Stability and Resilience in a Denitrifying Fluidized Bed Reactor. Microb. Ecol. 52: 311-321.
  14. Gentry, T., Wickham, G.S, C.W. Schadt, and J.-Z. Zhou. 2006. Microarray applications in microbial ecology research. Microb. Ecol., 52:159-175 (Invited).
  15. Gentry, T., and J.-Z. Zhou. 2006. Microarrays-based microbial detection and characterization. In Advanced Techniques in Diagnostic Microbiology, Edited by Yi-Wei Tang and Charles W. Stratton, pp 276-290. Springer, New York, NY (Invited).
  16. He, Q., K. Huang, Z. He, E. Alm, M. W. Fields, T. C. Hazen, A. Arkin, J. D. Wall, and J.-Z. Zhou. 2006. Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough Inferred from Global Transcriptional Analysis. Appl. Environ. Microbiol. 72:4370-4381. Supplementary Information 1 (xls)2 (xls)3 (pdf)
  17. Hwang, C., W. Wu, T. J. Gentry, J. Carley, S. L. Carroll, C. Schadt, D. Watson, P. M. Jardine, J.-Z. Zhou, R. F. Hickey, C. S. Criddle, and M.W. Fields. 2006. Changes in bacterial community structure correlate with initial operating conditions of a field­scale denitrifying fluidized bed reactor. Appl. Microbiol. Biotechnol. 71:748-760.
  18. Leaphart, A. B., D. K. Thompson, K. Huang, E. Alm, X. Wan, A. Arkin, S. D. Brown, L. Wu, T. Yan, X. Liu, G. S. Wickham, and J.-Z. Zhou. 2006. Transcriptome Profiling of Shewanella oneidensis Gene Expression Following Exposure to Acidic and Alkaline pH. J. Bacteriol. 188:1633-42. Suppl Material: Table S1 (zip); Table S2 (doc)
  19. Liebich, J., S. C. Chong, C. Schadt, Z. He, and J.-Z. Zhou. 2006. Improvement of oligonucleotide probe design criteria for the development of functional gene microarrays for environmental applications. Appl. Environ. Microbiol. 72:1688-1691. Supplemental Material (doc)
  20. Luo, F., J. Zhong, Y. Yang, J.-Z. Zhou. 2006. Application of Random Matrix Theory to Microarray Profiles for Discovering Functional Gene Modules. Physical Review E 73 (031924), 1-5.
  21. Luo, F., J. Zhong, Y. Yang, R. H. Scheuermann, and J.-Z. Zhou. 2006. Application of random matrix theory to biological networks. Physics Lett. A: 357: 420-423.
  22. Mukhopadhyay A., Z. He , E. J. Alm, A.P. Arkin, E.E. Baidoo, S.C. Borglin, W.Chen, T.C. Hazen, Q. He, H.Y.Holman, K. Huang, R. Huang, D.C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. D. Wall, J. Wei, Z. M Yang, H. Yen , J.-Z. Zhou and J.D. Keasling. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach. J. Bacteriol. 188: 4068-4078.
  23. Qiu, X., M. J. Daly, A. Vasilenko, M. V. Omelchenko, E. K. Gaidamakova, L. Wu, J.-Z. Zhou, G. W. Sundin and J. M. Tiedje. 2006. Transcriptome Analysis Applied to Survival of Shewanella oneidensis MR-1 Exposed to Ionizing Radiation and Comparison to Deinococcus radiodurans. J. Bacteriol. 188:1199-1204.
  24. Rodríguez-Martínez, E.M., E. X. Pérez, C.W. Schadt, J.-Z. Zhou, and A.A. Massol-Deyá. 2006. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer in Vega Baja, Puerto Rico. International Journal of Environmental Research and Public Health: 3:292-300.
  25. Roh, Y., H. Gao, H. Vali, D. W. Kennedy, Z. K. Yang, W. Gao, A. C. Dohnalkova, R. D. Stapleton, J. W. Moon, T. J. Phelps, J. K. Fredrickson, and, J.-Z. Zhou. 2006. Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium Shewanella sp. PV-4. Appl. Environ. Microbiol. 72:3236-3244.
  26. Schadt C. W., and J.-Z. Zhou. 2006. Advances in Microarrays for Soil Microbial Community Analyses. In: Soil Biology Volume 8: Nucleic Acids and Proteins in Soil (Nannipieri, P. & Smalla K., eds). Springer-Verlag, Pp189-203.
  27. Walker, C. B., S. S. Stolyar, N. Pinel, H. Yen, Z. He, J.-Z. Zhou, J. D. Wall, D. A. Stahl. 2006. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain. Environ. Microbiol. 8:1950-1959. Supplementary Material.
  28. Wan, X., J.- Z. Zhou, and D. Xu. 2006. CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. International Journal of General Systems 35:109-125.
  29. Wei, X., T. Yan, N. G. Hommes, X. Liu, L. Wu, C. McAlvin, M.G. Klotz, L.A. Sayavedra-Soto, J.-Z. Zhou, and D. J. Arp. 2006. Transcript profile of Nitrosomonas europaea during growth and ammonia/carbonate deprivation. FEMS Microbiology Lett. 257:76-83.
  30. Windt, W.D, H. Gao, W. Krömer, J. Dick, N. Boon, J.-Z. Zhou, and W. Verstraete. 2006. AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1. Microbiology 152: 721-729. Suppl Material (pdf)
  31. Wu*, L., X. Liu, C. W. Schadt, and J.-Z. Zhou*. 2006. Microarray-based analysis of sub-nanogram quantities of microbial community DNAs using Whole Community Genome Amplification (WCGA). Appl. Environ. Microbiol. 72:4931-4941. Suppl Material: file 1 (pdf); file 2 (pdf); file 3 (doc) (*equal contribution, The 11th of the top 20 papers most requested in 2006 October to December by AEM).
  32. Wu, W.M., J. Carley, T. Gentry, M. A. Ginder-Vogel, M. Fienen, T. Mehlhorn, H. Yan, S. Caroll, J. Nyman, J. Luo, M. E. Gentile, M. W. Fields, R. F. Hickey, D. Watson, S. Fendorf, J.-Z. Zhou, P. Kitanidis, P. M. Jardine, and C. S. Criddle. 2006. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability. Environ. Sci. Technol. 40: 3986-3995. Supplementary Information (pdf). (Most-Cited Article Published in 2006, Thomson Scientific (ISI) Essential Science Indicators, most citations through the period ending December 31, 2007: “Hot Paper” Achievement 2008, Thomson Scientific (ISI) Essential Science Indicators, most citations in a two-month period for a paper published within the past two years).
  33. Yan, T., J.-Z. Zhou, and C. Zhang. 2006. Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiol.Ecol. 57: 251-259.
  34. Zhou, X., and J.-Z. Zhou. 2006. Oligosaccharide microarrays fabricated on aminooxyacetyl functionalized glass surface for characterization of carbohydrate-protein interaction. Biosensors & Bioelectronics. Biosensors & Bioelectronics 21: 1451-1458.
  35. Zhou, X., J.-Z. Zhou. 2006. Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays. Proteomics, 6:1415-1426.
  36. Zhu, M., Q. Wu, Y. Yang, J.-Z. Zhou. 2006. A New Approach to Identify Functional Modules Using Random Matrix Theory. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 1:117-123.
  1. Beliaev, A. S., D. M. Stanek, J. A. Klappenbach, L. Wu, D. A. Saffarini, M. F. Romine, K. H. Nealson, J. K. Fredrickson, and J.-Z. Zhou. 2005. Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J. Bacteriol. 187:7138-7145. Suppl Material: Tables S1-2 (zip); Tables S3-12 (zip)
  2. Bencheikh-Latmani, R., S. M. Williams, L. Haucke, C. S. Criddle, L. Wu, J.-Z. Zhou, B. M. Tebo. 2005. Global Transcriptional Profiling of Shewanella oneidensis MR-1 During Cr(VI) and U(VI) Reduction. Appl. Environ. Microbiol. 71:7453-7460. Suppl Material (pdf)
  3. Fields, M.W., T. Yan, S. K. Rhee, S. L. Carroll, P. Jardine, C. S. Criddle and J.-Z. Zhou. 2005. Impacts on microbial communities and cultivable isolates from ground water contaminated with high levels of nitric acid–uranium waste. FEMS Microbiol. Ecol. 53: 417–428
  4. Gao, W., Y. Liu, J.-Z. Zhou, and H. Pan. 2005. Effects of a Strong Static Magnetic Field on Bacterium Shewanella oneidensis: An Assessment by Using Whole Genome Microarray. Bioelectromagnetics, 26:2-6.
  5. Gu, B., W. Wu, M. A. Ginder-Vogel, H. Yan, M. W. Fields, J.-Z. Zhou, S. Fendorf, C. S. Criddle, and P. M. Jardine. 2005. Bioreduction of Uranium in a Contaminated Soil Column. Environ. Sci. Technol. 39: 4841-4847.
  6. He, Z., L. Wu, M. W. Fields, J.-Z. Zhou. 2005. Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression. Appl. & Environ. Microbiol. 71: 5154–5162. Supplementary Information (xls)
  7. He, Z., L. Wu, X. Li, M. W. Fields, J.-Z. Zhou. 2005. Empirical establishment of oligonucleotide probe design criteria using perfect match and mismatch probes and artificial targets. Appl. & Environ. Microbiol, 71:3753-3760. Suppl Material: Figure S1 (zip); Tables (doc) (Listed as one of the top 20 papers most requested in 2005 by AEM).
  8. Kataeva, I., J. Chang, H. Xu, C. Luan, J.-Z. Zhou, V. N. Uversky, D. Lin, P. Horanyi, Z. Liu, L. G. Ljungdahl, J. Rose, M. Luo, and B. Wang. 2005. Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli. J. Proteome Res. 4:1942-1951.
  9. Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. Gorby, T. Holzman, J. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, X Qiu, M. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J.-Z. Zhou, F. W. Larimer, C. Lawrence, M. Riley, F. R. Collart, J. R. Yates, III, R. D. Smith, C. Giometti, K. Nealson, J. K. Fredrickson, and J. M. Tiedje. 2005. Global Profiling of Shewanella oneidensis MR-1: Expression of ‘Hypothetical’ Genes and Improved Functional Annotations. Proc. Nat. Acad. Sci.USA 102: 2099-2104. Suppl Material (link)
  10. Li, X., Z. He, and J.-Z. Zhou. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 33:6114-6123.
  11. Liu, Y., W. Gao, T. Yan, L. Wu, X. Liu, E. Alm, S. Wang, A. Arkin, M. W. Fields, D. K. Thompson, and J.-Z. Zhou. 2005. Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions. J. Bacteriol. 187: 2901-2907.
  12. Oda, Y., S. K. Samanta, L. Wu, X. Liu, T. Yan, J.-Z. Zhou, C. S. Harwood. 2005. A functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris. J. Bacteriol. 187: 7784-7794. Supplementary Information (pdf)
  13. Qiu, X., G. W. Sundin, L. Wu, J.-Z. Zhou, and J. M. Tiedje. 2005. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following UVA-, UVB- and UVC exposure. J. Bacteriol. 187: 3556-3564. Suppl Material: Text (doc); Figures (ppt)
  14. Stapleton, R., Z. L. Sabree, A. V. Palumbo, C. Moyer, A. Devol, Y. Roh, and J.-Z. Zhou. 2005. Metal reduction at cold temperatures by Shewanella isolates from various marine environments. Aquatic Microbiol. 38: 81–91.
  15. Wu, W., B. Gu, M. W. Fields, M. Gentile,Y. Ku, H. Yan, S. Tiquia, T. Yan, J. Nyman, J.-Z. Zhou, P.M. Jardine, C. S. Criddle. 2005. Uranium (VI) Reduction by Denitrifying Biomass. Bioremediation J., 9:49-61.
  1. Gao, H., Y. Wang, X. Liu, T. Yan, L. Wu, E. Alm, A. Arkin, D. K. Thompson, and J.-Z. Zhou. 2004. Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis. J. Bacteriol., 186: 7796-7803. SupplMat: Figure (doc), Table (xls)
  2. Liu, Y., A. Venkateswaran, and J.-Z. Zhou, 2004. Functional Genomic Analysis of Deinococcus radiodurans Resistance to Ionizing Radiation. European Symposium on Environmental Biotechnology on April 25-28, 2004.
  3. Luo, F., L. Khan, F. Bastani, I. Yen and J.-Z. Zhou. 2004. A Dynamically Growing Self-organizing Tree (DGSOT) for Hierarchical Clustering Gene Expression Profiles. Bioinformatics 20: 2605-2617.
  4. Palumbo, A.V., J. Schryver, M. Fields, C. Bagwell, and J.-Z. Zhou, T. Yan, X. Liu, and C. T. Brandt. 2004. Coupling of Functional Gene Diversity and Geochemical Data from Environmental Samples. Appl. Environ. Microbiol. 70:6525-6534.
  5. Post, V.M, R.C. Izaurralde, J.D. Jastrow, B.A. McCarl, J.E. Amonette, V.L. Bailey, P.M. Jardine, T.O. West, J.-Z. Zhou. 2004. Enhancement of Carbon Sequestration in U.S. Soils. BioScience 54: 895-908.
  6. Qiu, X., R. A. Hurt, L.. Wu, C. Chen, J. M. Tiedje, and J.-Z. Zhou. 2004. Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR. J. Microbiol. Methods 59:199-210.
  7. Rhee*, S.K, X. Liu, L. Wu, S. C. Chong, X. Wan and J.-Z. Zhou*. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-4317 (*Equal contribution).
  8. Schadt, C. W., J. Liebich, S. C. Chong, T. J. Gentry, Z. He, H. Pan and J.-Z. Zhou. 2004. Design and Use of Functional Gene Microarrays (FGAs) for the Characterization of Microbial Communities. In: Savidge T, Pothulakis H (eds) Methods in Microbiology V34: Microbial Imaging, pp331-368, Academic Press, London (Invited).
  9. Tiquia, S.M., M.W. Fields, and J.-Z. Zhou. 2004. Oligonucleotide-based functional gene arrays for analysis of microbial communities in the environment. In: Molecular Microbial Ecology Manual. Kowalchuk, G.G.; de Bruijn, F.J.; Head, I.M.; Akkermans, A.D.; van Elsas, J.D. (Eds.), Kluwer Academic Publishers, pp. 1743-1763.
  10. Tiquia, S.M., L.Wu, S.C. Chong, S. Passovets, D. Xu, Y. Xu, and J.-Z. Zhou. 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 36: 664-675.
  11. Wan, X., N.C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, L. Wu, X. Liu, T. Yan, A. Leaphart, R. L. Hettich, J.-Z. Zhou, and D. K. Thompson. 2004. Transcriptomic and proteomic characterization of the fur modulon in the metal-reducing bacterium Shewanella oneidensis. *Equal contribution. J. Bacteriol. 186: 8385-8400.
  12. Wan, X., D. Xu, A. Kleinhofs and J.-Z. Zhou. 2004. Quantitative relationship between synonymous codon usage bias and GC composition across the unicellular genomes. BMC Evolutionary Biology 2004, 4:19.
  13. Wu, L., D. K. Thompson, X. Liu, M. W. Fields, C. E. Bagwell, J. M. Tiedje, and J.-Z. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 38: 6775-6782. Supplementary Information (pdf)
  14. Ye, Q., Y. Roh, S. L. Carroll, B. Blair, J.-Z. Zhou, C. Zhang and M. W. Fields. 2004. Alkaline, anaerobic respiration: isolation and characterization of a novel, alkaliphilic, metal-reducing bacterium. Appl. Environ. Microbiol. 70: 5595-5602.
  15. Zhou, X., and J.-Z. Zhou. 2004. Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal. Chem. 76:5302-5312.
  16. Zhou, J.-Z., and D. K. Thompson. 2004. Microarray technology and applications in environmental microbiology. Vol 82. In: Sparks D.L. (Editor-in-Chief), Advances in Agronomy. Academic Press, New York pp 183-268 (Invited).
  17. Zhou, J.-Z., D.K. Thompson, Y. Xu, and James M. Tiedje. 2004. Microbial Functional Genomics. 624pp. John Wiley & Sons, Hoboken, New Jersey. (First comprehensive book in this field)
  18. Zhou, J.-Z., B. Xia, H. Huang, A.V. Palumbo, and J. M. Tiedje. 2004. Microbial diversity and heterogeneity in sandy subsurface soils. Appl. Environ. Microbiol. 70: 1723-1734.
  19. Zhou, X., L. Wu, J.-Z. Zhou. 2004. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir 20: 8877-8885.
  1. Liu, X., C. Bagwell, L. Wu, A. H. Devol, and J.-Z. Zhou. 2003. Molecular Diversity of Sulfate-Reducing Bacteria from Two Different Continental Margin Habitats. Appl. Environ. Microbiol. 69:6073-6081 (*Equal contribution).
  2. Liu, X., S. M. Tiquia, G. Holguin, L. Wu, S. C. Nold, A. H. Devol, K. Luo, A. V. Palumbo, J. M. Tiedje, and J.-Z. Zhou. 2003. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen deficient zone of the Pacific Coast of Mexico. Appl. Environ. Microbiol. 69:3549-3560.
  3. Liu*, Y., J.-Z. Zhou*, M. Omelchenko, A. Beliaev, A. Venkateswaran, J. Stair, L. Wu, D. K. Thompson, D. Xu, I. B. Rogozin, E. K. Gaidamakova, M. Zhai, K. S. Makarova, E. V. Koonin, and M. J. Daly. 2003. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. PNAS, 100: 4191-4196. *equal contribution. (Commentary by Jeremy S.Edwards and John R. Battista. 2003. TRENDS in Biotechnology: 21: 381-382).  Supplemental Information (website)
  4. Palumbo, A.V., S. Fisher, J. R. Tarver, W. L. Daniels, Z. Yang, S. M. Tiquia, L. Wu, and J.-Z. Zhou, and J. Amonette,. 2003. Issues with the Use of Fly Ash for Carbon Sequestration Proceedings of the Second National Conference on Carbon Sequestration. Hilton Mark Center, Alexandria, Virginia. May 5-8, 2003.
  5. Roh, Y., C. Zhang, H. Vali, R.J. Lauf, J.-Z. Zhou, and T. J. Phelps. 2003. Biogeochemical and environmental factors in Fe biomineralization: magnetite and siderite formation. Clays and Clay Minerals. 51: 83-95.
  6. Treves, D. S., B. Xia, J.-Z. Zhou and J. M. Tiedje. 2003. A Two-Species Test of the Hypothesis That Spatial Isolation Influences Microbial Diversity in Soil. Microb. Ecol. 45:20-8.
  7. Wan, X., D. Xu, and J.-Z. Zhou. 2003. A new informatics method for measuring synonymous codon usage bias. In: Intelligent engineering systems through artificial neural networks, vol 13, eds. Dagli et al., p1101-1018. New York, NY: ASME Press
  8. Yan, T., M. W. Fields, L. Wu, Y. Zu, J. M. Tiedje and J.-Z. Zhou. 2003. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ. Microbiol. 5:13-24 (*equal contribution).
  9. Yost, C., L. Hauser, F. Larimer, D.K. Thompson, A. Beliaev, J.-Z. Zhou, Y. Xu, and D. Xu. 2003. A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins. Omics 7:177-191.
  10. Zhou, J.-Z. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opion. Microbiol. 6:288-294 (Invited).
  11. Zhou, J.-Z., and D. K. Thompson. 2003. Microarrays: Application in environmental microbiology. p. 1968-1979. Bitton, G. (Editor in Chief), The Encyclopedia in Environmental Microbiology, John Wiley & Sons, New York. (Invited)
  12. Zhou, J.-Z., B. Xia, H. Huang, D. S. Treves, L. J. Hauser, R. J. Mural, A. V. Palumbo, and J. M. Tiedje. 2003. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biol. Biochem. 35:915-924.
  1. Beliaev, A. S., D. K. Thompson, C. S. Giometti, G. Li, J. Yates III, K. H. Nealson, J.M. Tiedje, J. F. Heidelberg, and J.-Z. Zhou. 2002. Gene and Protein Expression Profiles of Shewanella oneidensis During Anaerobic Growth with Different Electron Acceptors. Omics: A Journal of Integrative Biology 6: 39-60.
  2. Beliaev, A. S., D. K. Thompson, M. Fields, L. Wu, D. P. Lies, K. H. Nealson, and J.-Z. Zhou. 2002. Microarray Transcription Profiling of a Shewanella oneidensis etrA Mutant. J. Bacteriol. 184: 4612-4616.
  3. Gu, B., D. B. Watson, L. Wu, D. H. Phillips, D. C. White, and J.-Z Zhou. 2002. Microbiological characteristics in a zero-valent iron reactive barrier. Environ. Monitoring Assessment: 77: 293-309.
  4. Palumbo A. V., J.-Z. Zhou, C. Zhang, R. D. Stapleton, B. L. Kinsall, and T. M. Phelps. 2002. Biotransformations and biodegradation in extreme environments. P. 549-571. In Biotransformations: Bioremediation Technology for Health and Environmental Protection (eds. Singh, V. P. and Stapleton, R. D.). Elsevier, London.
  5. Roh, Y., S. Liu, G. Li, H. Huang, T. J. Phelps, and J.-Z. Zhou. 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments. Appl. Environ. Microbiol., 68:6013-6020.
  6. Schut, G. J., J.-Z. Zhou, and M. W. Adams. 2002. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex. J. Bacteriology 183: 7027-7036.
  7. Taranenko N. I., R. Hurt, J.-Z. Zhou, N. R. Isola, H. Huang, S.H. Lee, C. H. Chen. 2002. Laser desorption mass spectrometry for microbial DNA analysis. J. Microbiol. Methods 48: 101-106.
  8. Thompson, D.K., A. S. Beliaev, C. S. Giometti, S. L. Tollaksen, T. Khare, D. P. Lies, K. H. Nealson, H. Lim, J. Yates III, C. C. Brandt, J. M. Tiedje, and J.-Z. Zhou. 2002. Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress. Appl. Environ. Microbiol. 68:881-892.
  9. Xu, D., G. Li, L. Wu, J.-Z. Zhou, and Y. Xu. 2002. PRIMEGENS: A Computer Program for Robust and Efficient Design of Gene-Specific Targets on Microarrays. Bioinformatics, 18:1432-1437, 2002.
  10. Zhou, J.-Z., and J. H. Miller. 2002. Microbial genomics, challenges and opportunities, The 9th International Conference on Microbial Genomes. J. Bacteriol. 184: 4327-4333 (Invited).
  11. Zhou, J.-Z., and D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opion. Biotech. 13:204-207. (Invited)
  12. Zhou, J.-Z., and J. M. Tiedje. 2002. New DOE program expands dramatically beyond microbial genomics. ASM News: 68:110-111 (Invited).
  13. Zhou, J.-Z., B. Xia, D. S. Treves, T. L. Marsh, R. V. O’Neill, L. Wu, A. V. Palumbo and J. M. Tiedje. 2002. Spatial and resource factors influencing high soil microbial diversity. Appl. Environ. Microbiol. 68: 326-334.
  1. Gruntzig, V., S. C. Nold, J.-Z. Zhou, and J. M. Tiedje. 2001. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Appl. Environ. Microbiol. 67: 760-768.
  2. Hurt, R. A., X. Qiu, L. Wu, Y. Roh, A. V. Palumbo, J. M. Teidje, and J.-Z. Zhou. 2001. Simultaneous Extraction of RNA and DNA from Environmental Samples. Appl. Environ. Microbiol. 67: 4495-4503.
  3. Murray, A. E., D. Lies, G. Li, K. Nealson, J.-Z. Zhou, J. M. Tiedje. 2001. DNA:DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Sci. Acad. USA 98: 9853-9858. Supplemental Information: Table 2 (xls), Fig 4 (website), Fig 5 (website)
  4. Qiu, X., L. Wu, H. Huang, P. E. McDonel, A.V. Palumbo, J. M. Tiedje, and J.-Z. Zhou. 2001. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67: 880-887.
  5. Schut, G. J., J.-Z. Zhou, and M. W. W. Adams. 2001. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex. J. Bacteriology 183: 7027-7036
  6. Sepulveda-Torres, L. C., J.-Z. Zhou, C. Guasp, J. Lalucat, D. Knaebel, J. L. Plank and C. S. Criddle. 2001. Pseudomonas strain KC represents a new genomovar within Pseudomonas stutzeri. Int. Syst. J. Bact. 51: 2013-2019.
  7. Tiedje, JM, JC Cho, A Murray, D Treves, B Xia, and J Zhou. Soil teeming with life: new frontiers for soil science. In: (eds RM Rees, BC Ball, CD Campbell, CA Watson) Sustainable Management of Soil Organic Matter. CAB International.
  8. Wu, L., D. Thompson, G. Li, R. Hurt, H. Huang, J. M. Tiedje, and J.-Z. Zhou. 2001. Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment. Appl. Environ. Microbiol. 67: 5780-5790.
  9. Xia, B., D. S. Treves, J.-Z. Zhou, J. M. Tiedje. 2001. Soil microbial community diversity and driving mechanisms. Prog. Nat. Sci. 11: 818-824.
  10. Zhang, C., J. Horita, D. R. Cole, J.-Z. Zhou, D. R. Lovley, and T. J. Phelps. 2001. Temperature-dependent oxygen and carbon isotope fractions of biogenic siderite. Geochimica et Cosmochimica Acta. 65: 2257-2271.
  11. Zhou, J.-Z., S. Liu, B. Xia, C. Zhang, A. V. Palumbo, and T. J. Phelps. 2001. Molecular characterization and diversity of thermophilic iron-reducing enrichment cultures from deep subsurface environments. J. Appl. Microbiol. 90: 96-105.
  1. Braker, G., J.-Z. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje. 2000. Nitrite Reductase Genes (nirK and nirS) as Functional Markers to Investigate Diversity of Denitrifying Bacteria in Marine Sediment Communities. Appl. Environ. Microbiol. 66: 2096-2104.
  2. Nold, S. C., J.-Z. Zhou, A. H. Devol, and J. M. Tiedje. 2000. Pacific Northwest marine sediments contain-Proteobacterial ammonia oxidizing bacteria. Appl. Environ. Microbiol. 66: 4532-4535.
  3. Xia, B., J.-Z. Zhou, J. M. Tiedje. 2000, Structure of bacterial community in soil environment and its ecological characteristics, Acta Ecologica Sinica 20(4): 1201-1209.
  4. Xu, D., Y. Xu, G. Li, and J.-Z. Zhou. 2000. A computer program for generating gene-specific fragments for microarrays. P. 3-4, In Miyano, S., R. Shamir, and T. Takagi (eds), Currents in Computational Molecular Biology, Universal Academy Press, Inc, Tokyo, Japan.
  5. Zhou, J.-Z. and A. V. Palumbo. 2000. Sequence to function: The 7th Conference on Small Genomes. Genetica 108: vii-ix.
  6. Zhou, J.-Z., B. Xia, L. Wu, R. V. O’Neill, A. V. Palumbo, and J. M. Tiedje. 2000. Unusual diversity in soil microbial communities. The 6th Chinese Society of Ecology. P. 29-40 (Invited).
  1. Li, G., and J.-Z Zhou. 1999. Genomics, microarray-based genomic technology and potential ecological applications. The 3rd Conference on Molecular Ecology, Beijing, P. 29-40 (Invited).
  2. Palumbo, A. V., J.-Z. Zhou, T. J. Phelps, B. Kinsall, C. Zhang, E. L. Majer, J. E. Peterson, T. Griffin, S. M. Pfiffner. 1999. Ecology and bioremediation: a staged approach to site characterization. Uzochukwu and Reddy (eds), Proceedings of the 1998 National Conference on Environmental Remediation Science and Technology. Battelle Press, pp. 195-202.
  3. Song, B., M. M. Haggblom, J.-Z. Zhou, J. M. Tiedje, and N. J. Palleroni. 1999. Taxonomic characterization of aromatics-degrading denitrifying bacteria: Description of Azoarcus sp. nov. and Azoarcus sp. nov. Int. Syst. J. Bact. 49: 1129-1140.
  4. Zhang C., R. Stapleton, J.-Z. Zhou, A. V. Palumbo, and T. J. Phelps. 1999. Iron reduction by psychrophilic enrichment cultures. FEMS Microb. Ecol. 30: 367-371.
  5. Zhou. J.-Z., A. V. Palumbo and J. M. Strong-Gunderson. 1999. Phylogenetic characterization of a mixed microbial community capable of degrading carbon tetrachloride. Appl. Biochem. Biotechnol. 80: 243-253.
  6. Dedysh, S. N., N. S. Panikov, W. Liesack, R. Grobkopf, J.-Z. Zhou, and J. M. Tiedje. 1998. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science 282: 281-284.
  7. Xia, B., J.-Z. Zhou, J. M. Tiedje 1998. Effect of vegetation on structure of soil microbial community. Chinese Journal of Applied Ecology 9(3): 296-300
  8. Xia, B., J.-Z. Zhou, J. M. Tiedje. 1998. Application of molecular methods in microbial ecology. Acta Scientiarum Naturalium Universitatis Sunyatseni 37(2): 97-101
  9. Xia, B., J.-Z. Zhou, J. M. Tiedje. 1998. Effect of overlying vegetation on soil microbial community structure and their activity. Acta Scientiarum Naturalium Universitatis Sunyatseni 37(3): 94-98
  10. Zhou, J.-Z., S. V. Liu, C., Zhang, A. V. Palumbo, and T. J. Phelps. 1998. Extremophilic iron-reducing bacteria: Their implications for possible life in extraterrestrial environments. The Third Symposium of Chinese Young Scientists, p. 47-52, Beijing, P. R. China.
  11. Liu, S., J.-Z. Zhou, C. Zhang, D. R. Cole and T. J. Phelps. 1997. Thermophilic Fe(III)-reducing bacteria from the deep subsurface: The evolutionary implications. Science 277: 1106-1109.
  12. Massol-Deya, A., R. Weller, L. Rio-Hernandez, J.-Z. Zhou, R. F. Hickey, and J. M. Tiedje. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl. Environ. Microbiol. 63: 270-276.
  13. Tiedje, J.M., K. Nüsslein, J.-Z. Zhou, B. Xia, C. Moyer, and F. Dazzo. 1997. The vast world of microbial diversity. In The 5th International Symposium on New Frontiers in Microbiology by the Japan Science and Technology Corporation. January 30-31, 1997, Tokyo, Japan.
  14. Tiedje, J. M., J.-Z. Zhou, K. Nusslein, C. Moyer and R. R. Fulthorpe. 1997. Extent and patterns of soil microbial diversity. P. 35-41. In Martins, M. T. et al. (eds). Progress in Microbial Ecology, Brazilian Society for Microbiology, Sao Paulo.
  15. Zhou, J.-Z., M. E. Davey, J. B. Figueras, E. Rivkina, D. Gilichinsky, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913-3919.
  16. Zhou, J.-Z., A. V. Palumbo, and J. M. Tiedje. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus using SSU rRNA primers and probes. Appl. Environ. Microbiol. 63: 2384-2390.
  17. Chee-Sanford, J.C., J. W. Frost, M. R. Fries, J.-Z. Zhou, and J. M. Tiedje. 1996. Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Appl. Environ. Microbiol. 62: 964-973.
  18. Shih, C. C., M. E. Davey, J.-Z. Zhou, J. M. Tiedje, and C. S. Criddle. 1996. Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene. Appl. Environ. Microbiol. 62: 2953-2960.
  19. Tiedje, J. M., and J.-Z. Zhou. 1996. Analysis of non-culturable bacteria. pp. 53-65. In Methods for the examination of organismal diversity in soils and sediments, (G. S. Hall, ed). CAB International, New York.
  20. Zhou, J.-Z., and A. Kleinhofs. 1996. Molecular evolution of nitrate reductase genes. J. Mol. Evol. 42: 432-442.
  21. Zhou, J.-Z., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322. (Among the most highly cited 20 papers for all papers published in Applied and Environmental Microbiology, since January, 2008)
  22. Zhou, J.-Z., S. Ma, and G. W. Hinman. 1996. Ecological exergy analysis: A new method for ecological energetics study. Ecological Modeling 84: 291-303.
  23. Zhou, J.-Z., M. R. Fries, J. C. Chee-Sanford, and J. M. Tiedje. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene: Description of Azoarcus tolulyticus sp. nov. Int. J. Syst. Bacterol. 45: 500-506.
  24. Zhou, J.-Z., A. Kilian, R. L. Warner, and A. Kleinhofs. 1995. Variation of nitrate reductases genes in grass species. Genome 38: 919-927.
  25. Zhou, J.-Z., and J. M. Tiedje. 1995. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol. Ecol. 4: 613-638.
  26. Zhou, J.-Z., and J. M. Tiedje. 1995. Development of phylogenetic probes specific to Burkholderia cepacia G4. pp. 65-75. In Hinchee, R. E., Douglas, G. S. and Ong, S. K. (eds), Monitoring and Verification of Bioremediation, Battle Press, Columbus.
  27. Fries, M. R., J.-Z., Zhou, J. C. Chee-Sanford, and J. M. Tiedje. 1994. Isolation, characterization and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60: 2802-2810.
  28. Zhou, J.-Z., A. Kilian, R. L. Warner, and A. Kleinhofs. 1994. An NADH nitrate reductase gene copy appears to have been deleted in barley. Theor. Appl. Genetics 88: 589-592.
  29. Zhou, J.-Z., S. Ma, and C. Chen. 1991. An index of ecosystem diversity. Ecol. Modeling 59: 151-163.
  30. Zhou, J.-Z. and S.Ma. 1990. Ecosystem stability. pp. 54-71. In Perspectives on Modern Ecology, Edited by Shijun M. China Science and Technology Press.
  31. Zhou, J.-Z. 1987. On ecological engineering. The proceeding of Symposium of Ecological Society of China. Chengdu, China.
  32. Zhou, J.-Z., and C. Chen. 1987. Predation of wolf spider Lycosa pseudoannulata to brown planthopper Nilaparvata lugens and simulation models there of: 3. Selective predation. Acta Ecologia Sinica 7: 228-237. (Chinese)
  33. Zhou, J.-Z., and C. Chen. 1987. Studies on predation and simulation models of Wolf spider Lycosa pseudoannulata to Brown planthopper Nilaparvata lugens IV. Simulation model and stability analysis of the monopredator-two prey species system. Acta Ecologia Sinica 7: 349-358. (Chinese)
  34. Zhou, J.-Z., and C.. Chen. 1987. Quantitative measurement of selectivity of predator for prey. Acta Ecologia Sinica, 7: 50-56. (Chinese)
  35. Zhou, J.-Z., and C. Chen. 1987. Studies on predation and simulation models of Cyrtarrhinus lividipennis to Brown planthopper Nilaparvata lugens. Hunan Agri. Sci. 36: 35-46. (Chinese)
  36. Zhou, J.-Z. 1986. A general model for insect population simulation. The proceeding of the Symposium of Youth Ecologists of China, Zhangjiajie, China.
  37. Zhou, J.-Z., and C. Chen. 1986. Studies on predation and simulation models of Wolf spider Lycosa pseudoannulata to Brown planthopper Nilaparvata lugens I. Functional response. Chinese J. Biol. Control, 2(1): 2-9. (Chinese)
  38. Zhou, J.-Z., and C.M. Chen. 1986. Studies on predation and simulation models of Wolf spider Lycosa pseudoannulata to Brown planthopper Nilaparvata lugens II. Simulation model and stability analysis of the monopredator-monoprey species system. Acta Ecologia Sinica 6: 238-247. (Chinese)