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Publications

  1. Deng Y, D Ning, Y Qin, K Xue, L Wu, Z He, H Yin, Y Liang, V Buzzard, ST Michaletz, and J Zhou. Spatial scaling of forest soil microbial communities across a temperature gradient. Environ Microbiol. doi.org/10.1111/1462-2920.14303. Supplemental Information; Supplmental Data: R code R file
  2. Guo X, J F eng, 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. Climate Warming Leads to Divergent Succession of Grassland Microbial Communities. Nat Clim Change. In press.
  3. 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 tundra. Glob Change Biol. https://doi.org/10.1111/gcb.14325.
  4. 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 productivity. Glob Change Biol. https://doi.org/10.1111/gcb.14333. In press.
  5. 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 stability. Environ Microbiol. doi.org/10.1111/1462-2920.14239
  6. 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 microcosm. Environ Microbiol. doi.org/10.1111/1462-2920.14366
  7. Yu H, Z H e, J Van Nostrand, S Wang, D Jin, A Wang, L Wu, D Wang, X Tai, J Zhou, and Y Deng. Elevated CO2 and warming altered grassland microbial communities in soil top-layers. Front Microbiol. In press.

2018

  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 microbiome. Environ. Sci Technol 52:6526-6533.
  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 therapy. ISME J. 12:1210–1224.
  3. Christense n 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 composition. PLoS ONE 13(3): e0194663.
  4. 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 suppression. PLoS ONE 13: e0196581.
  5. 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)
  6. 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.
  7. 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 functioning. mBio. 9:e02435-17. Supplementary Information (csv)
  8. 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 pretreatment. Process Biochem. 64:1-8.
  9. 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.
  10. 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.
  11. 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 input. Nat Comm. 8:3175.
  12. 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.
  13. 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 forests. Funct Ecol. 32:61-70.
  14. 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.
  15. 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.
  16. 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.
  17. 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
  18. Wu B, F Liu, MD Weiser, D Ning, JG Okie, L Shen, J Li, B Chai, Y Deng, K Feng, L Wu, S Chen, J Zhou, and Z He. Temperature determines the diversity and structure of N2O-reducing microbial assemblagesFunct. Ecol. 32:1867-1878.
  19. Wu X, L Wu , Y Liu, P Zhang, Q Li, J Zhou, N Hess, TC Hazen, W Yang and R Chakraborty. 2018. Microbial interactions with dissolved organic matter drive carbon dynamics and community successionFront Microbiol. doi: 10.3389/fmicb.2018.01234. 9:1234.
  20. Xiao, J., F. Yu, W. Zhu, C. Xu, K. Zhang, Y. Luo, J. M. Tiedje, J.-Z. Zhou, L. Cheng. 2018. Comment on “The whole-soil carbon flux in response to warming”.Science, 359:eaao0218. DOI: 10.1126/science.aao0218
  21. Xing W, J Li, P Li, C Wang, Y Cao, D Li, Y Yang, J Zhou, and J Zuo. 2018. Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities. J Envrion Sci. 65:262-270. 
  22. 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 stand. Environ Poll. 242(A):229-238.
  23. Yang S, AM Brandon, JCA Flanagan, J Yang, D Ning, S Cai, H Fan, Z Wang, J Ren, E Benbow, N Ren, RM Waymouth, J Zhou, CS Criddle, and W Wu. 2018. Biodegradation of polystyrene wastes in yellow mealworms (larvae of Tenebrio molitor Linnaeus): Factors affecting biodegradation rates and the ability of polystyrene-fed larvae to complete their life cycle. Chemosphere. 191:979-989.
  24. Yu H, Z He, A Wang, J Xie, L Wu, JD Van Nostrand, D Jin, Z Shao, CW Schadt, J Zhou, and Y Deng. 2018. Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers. Appl. Environ Microbiol. 84:e01698-17.
  25. Yuan M, J Zhang, K Xue, L Wu, Y Deng, J Deng, L Hale, X Zhou, Z He, Y Yang, JD Van Nostrand, EAG Schuur, KT Kostantinidis, CR Penton, JR Cole, JM Tiedje, Y Luo, and J Zhou. 2018. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. Glob Change Bio. 24:297-307.
     
  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 communities. ISME J. 11:1825-1835. doi: 10.1038/ismej.2017.48.
  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 toposequence. Sci Rep. 7:9604. Doi:10.1038/s41598-017-07639-1.
  3. Escalas, A., Troussellier, M., Tong, Y., Bouvier, T., Bouvier, C., Mouchet, M. A., Flores hernandez, D., Ramos miranda, J., Zhou, J. and Mouillot, D. Functional diversity and redundancy across fish gut, sediment, and water bacterial communities. Environ. Microbiol. 19:3268-3282.
  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 warming. Glob Change Biol. https://doi.org/10.1111/gcb.13755
  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 locations. PloS One, 12(5): e0176696. doi.org/10.1371/journal.pone.0176696.  Supplementary Data: Fasta files (zip)
  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. doi.org/10.1016/j.watres.2017.08.055
  7. Huang C, Q Liu, C Chen, F Chen, YK Zhao, LF Gao, WZ Liu, JZ Zhou, ZL Li, AJ Wang. Elemental sulfur recovery and spatial distribution of functional bacteria and expressed genes under different carbon/nitrate/sulfide loadings in up-flow anaerobic sludge blanket reactors. J Haz Mat. 324A:48-53.
  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 forest. Ecology. 98:2019-2028.
  9. King AJ, SP Preheim, KL Bailey, MS Robeson, TR Chowdhury, BR Crable, RA Hurt Jr, T Mehlhorn, KA Lowe, TJ Phelps, AV Palumbo, CC Brandt, SD Brown, M Podar, P Zhang, WA Lancaster, F Poole, DB Watson, MW Fields, JM Chandonia, EJ Alm, J Zhou, MWW Adams, TC Hazen, AP Arkin, and DA Elias. 2017. Temporal dynamics of in-field bioreactor populations reflect the groundwater system and respond predictably to perturbation. Environ. Sci. Technol., 51(5):2879–2889.
  10. Kuang J, Cadotte MW, Chen Y, Shu H, Liu J, Chen L, Hua Z, Shu W, Zhou J and Huang L 2017. Conservation of species- and trait-based modeling network interactions in extremely acidic microbial community assembly. Front. Microbiol. 8:1486. doi: 10.3389/fmicb.2017.01486
  11. Li H, S Yang, Z Xu, Q Yan, X Li, JD Van Nostrand, Z He, F Yao, X Han, J Zhou, Y Deng, Y Jiang. 2017. Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation. Soil Biol Biochem. 104:18-29.
  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 groundwater. Water Res. 123:268-276.
  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, Utah. Geobiology. 15:131-145. DOI: 10.1111/gbi.12201.
  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 acids. FEMS Microbiol Ecol 93(4):fix040 doi: 10.1093/femsec/fix040.
  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 deposition. Mol Ecol. 26:4186-4196.
  16. Navarrete, AA, EV Mellis, A Escalas, LN Lemos, J Lavres Jr, JA Quaggio, J Zhou, SM Tsai. 2017. Zinc concentration affects the functional groups of microbial communities in sugarcane-cultivated soil. Agricult. Ecosys. Environment 236:187-197.
  17. Tu Q, Z He, L Wu, K Xue, G Xie, P Chain, PB Reich, SE Hobbie, and J Zhou. 2017. Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem. Soil Biol Biochem. 106:99-108.
  18. Tu Q, J Li, Z Shi, Y Chen, L Lin, J Li, H Wang, J Yan, Q Zhou, X Li, L Li, J Zhou, Z He. 2017. HuMiChip2 for strain level identification and functional profiling of human microbiomes. Appl Microbiol Biotechnol. 101:423-435.
  19. Wang, H, L Yu, Z Zhang, W Liu, L Chen, G Cao, H Yue, J Zhou, Y Yang, Y Tang and J He. 2017. Molecular mechanisms of water table lowering and nitrogen deposition in affecting greenhouse gas emissions from a Tibetan alpine wetland Global Change Biol. 23, 815–829.
  20. Wang, J., Meier, S., Soininen, J., Casamayor, E. O., Pan, F., Tang, X., Yang, X., Zhang, Y., Wu, Q., Zhou, J. and Shen, J. 2017, Regional and global elevational patterns of microbial species richness and evenness. Ecography, 40: 393–402. doi:10.1111/ecog.02216
  21. 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 drylands. ISME J. 11:1345-1358.
  22. Wang, Y., R Zhang, Z He, JD Van Nostrand, Q Zheng, J Zhou, and N Jiao. 2017. Functional gene diversity and metabolic potential of the microbial community in an estuary-shelf environment. Front. Microbiol. 8:1153, DOI: 10.3389/fmicb.2017.01153  Supplementary Data: Microarray data - original signal (txt)Microarray data - Relative Signal (csv)
  23. 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 Platform. PLoS One, 12(4):e0176716. doi: 10.1371/journal.pone.0176716.
  24. Wu L, Y Yang, S Chen , J Shi, M Zhao, Z Zhu, S Yang, Y Qu, Q Ma, Z He, J Zhou, and Q He. Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters. ISME J doi: 10.1038/ismej.2017.135
  25. 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 cooling. ISME J. 11:2102-2111.
  26. 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.
  27. Yan, Q., J. Stegen, Y. Yu, Y. Deng, X. Li, S. Wu, L. Dai, X. Zhang, J. Li, C. Wang, J. Ni, X. Li, H. Hu, F. Xiao, W. Feng, D. Ning, Z. He, J. D. van Nostrand, L. Wu, and J.-Z. Zhou. 2017. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Mol. Ecol. 26:3839-3850.
  28. Yang, S., Y. Zhang, J. Cong, M. Wang, M. Zhao, H. Lu, C. Xie, C. Yang, T. Yuan, D. Li, J.-Z. Zhou, B. Gu, Y. Yang. 2017. Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones. Front. Microbiol. doi: 10.3389/fmicb.2017.00200.
  29. Yang Z, S Yang, J Van Nostrand, J Zhou, W Fang, Q Qi, Y Liu, L Liang, SD Wullschleger, DE Graham, Y Yang, and B Gu. Microbial community and functional gene changes in Arctic tundra soils in a microcosm warming experiment. Front. Microbiol. In press.
  30. Yu D, M Xia, L Zhang, Y Song, Y Duan, T Yuan, M Yao, L Wu, C Tian, Z Wu, X Li, J Zhou and D Qiu. RpoN (σ54) is required for floc formation but not for extracellular polysaccharide biosynthesis in a floc-forming Aquincola tertiaricarbonis strain. Appl Environ Microbiol. doi: 10.1128/AEM.00709-17.
  31. Zeng, F., Z. Wang, Y. Wang, J.-Z. Zhou, and T. Chen. 2017. Large-scale 16S gene assembly using metagenomics shotgun sequences. Bioinformatics, 33:1447-1456. DOI:10.1093/bioinformatics/btx018
  32. Zhang J, Q Gao, Q Zhang, T Wang, H Yue, L Wu, J Shi, Z Qin, J Zhou, J Zuo and Y Yang. 2017. Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space. Microbiome. 5:57.
  33. Zhang, P., Z. He, J. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q., Tu, J. Wang, C. Schadt, M. Fields, T. Hazen, A. Arkin, D. Stahl, and J.-Z. Zhou. 2017. Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environ. Sci. & Technol. 51(7):3609–3620.
  34. Zhang Y, X Liu, J Cong, H Lu, T Sheng, X Wang, D Li, X Liu, H Yin, J Zhou, and Y Deng. The microbially-mediated soil organic carbon loss under degenerative succession in an alpine meadow. Mol Ecol. 26:3676-3686. 
  35. Zhou J and D Ning. 2017. Stochastic community assembly: Does it matter in microbial ecology? Microbiol Mol Biol Rev. 81:e00002-17.
  1. Bouskill, NJ, TE Wood, R Baran, Z Ye, BP Bowen, H-C Lim, J Zhou, JD Van Nostrand, P Nico, TR Northen, WL Silver, and EL Brodie. 2016. Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism (pdf). Front. Microbiol. 7:525. doi: 10.3389/fmicb.2016.00525
  2. Bracho R, S Natali , E Pegoraro, KG Crummer, C Schädel, G Celis, L Hale, L Wu, H Yin, JM Tiedje, KT Konstantinidis, Y Luo, J Zhou, EAG Schuur. 2016. Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations. Soil Biol Biochem. 97:1-14.
  3. Deng Y, Z He, J Xiong, H Yu, MY Xu, SE Hobbie, PB Reich, CW Schadt, A Kent, E Pendall, M Wallenstein, and J-Z Zhou. 2016. Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities. Glob Change Biol. 22:957-964.
  4. Deng Y, P Zhang, Y Qin, Q Tu, Y Yand, Z He, CW Schadt, and J-Z Zhou. 2016. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environ Microbiol. 18:205-218.
  5. Feng W, Z Shi, J Jiang, J Xia, J Liang, J Zhou, and Y Luo. 2016. Methodological uncertainty in estimating carbon turnover times of soil fractions. Soil Biol Biochem. 100:118–124
  6. Hemme, CL, SJ Green, L Rishishwar, O Prakash, A Pettenato, R Chakraborty, AM Deutchbauer, JD Van Nostrand, L Wu, Z He, IK Jordan, TC Hazen, AP Arkin, JE Kostka, and J-Z Zhou. 2016. Lateral Gene Transfer in a Heavy Metal-Contaminated Groundwater Microbial Community (pdf). mBio, 7:e02234-15
  7. Herath, A., B. Wawrik, Y. Qin, J.-Z . Zhou, and A.V. Callaghan. 2016. Transcriptional response of Desulfatibacillum alkenivorans AK-01 to growth on alkanes: insights from RT-qPCR and microarray analyses. FEMS Microbiology Ecology, 92: fiw062; DOI: 10.1093/femsec/fiw062.
  8. Hou Y, H Liu, J Han, W Cai, J Zhou, A Wang, and H Cheng. 2016. Electroactive Biofilm Serving as the Green Synthesizer and Stabilizer for in Situ Fabricating 3D Nanopalladium Network: An Efficient Electrocatalyst. ACS Sustainable Chem Engineer. 4:5392-5397.
  9. Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Detter JC, Glavina del Rio T, Hammon N, Israni S, Dalin E, Tice H, Pitluck S, Chertkov O, Brettin T, Bruce D, Han C, Schmutz J, Larimer F, Land ML, Hauser L, Kyrpides N, Mikhailova N, Ye Q, Zhou J, Richardson P, Fields MW. 2016. Complete genome sequence of Alkaliphilus metalliredigens strain QYMF, an alkaliphilic and metal-reducing bacterium isolated from borax-contaminated leachate ponds. Genome Announc 4(6):e01226-16. doi:10.1128/genomeA.01226-16.
  10. Huang C, Z Lia, F Chena, Q Liua, Y Zhao, L Gao, C Chena, J-Z Zhou, and A Wang. 2016. Efficient regulation of elemental sulfur recovery through optimizing working height of upflow anaerobic sludge blanket reactor during denitrifying sulfide removal process. Bioresource Technol. 200:1019-1023.
  11. Jiang Y, Y Liang, C Li, F Wang, YSui, N Suvannang, J Zhou, and B Sun. 2016. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol. Biochem. 95:250-261.
  12. Jiang Z, P Li, J Van Nostrand, P Zhang, J-Z Zhou, Y Wang, X Dai, R Zhang, D Jiang, and Y Wang. 2016. Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring (pdf). Sci Reports. 6:25262. doi:10.1038/srep25262
  13. Johnston, ER, LM Rodriguez-R, C Luo, MM Yuan, L Wu, Z He, EAG Schuur, Y Luo, JM Tiedje, J Zhou, and KT Konstantinidis. 2016. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem Front. Microbiol. 7:579.
  14. Kuang J, L Huang, Z He, L Chen, Z Hua, P Jia, S Li, J Liu, J Li, J Zhou, and W Shu. 2016. Predicting taxonomic and functional structure of microbial communities in acid mine drainage (pdf). ISME J. 10:1527–1539.  Supplementary data: Microarray data
  15. Liang B, D Kong, J Ma, C Wen, T Yuan, DJ Lee, J Zhou, A Wang. 2016. Low temperature acclimation with electrical stimulation enhance the biocathode functioning stability for antibiotics detoxification. Water Res. 100:157-168.
  16. Liang Y., H. Zhao, Y. Deng, J.-Z. Zhou, G. Li, and B. Sun. 2016. Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes (pdf). Front. Microbiol. 7:60. doi:10.3389/fmicb.2016.00060. Supplemental Data: Microarray data
  17. Michaletz ST, MD Weiser, NG McDowell, J Zhou, M Kaspari, BR Helliker, and BJ Enquist. 2016. The energetic and carbon economic origins of leaf thermoregulation. Nat Plants 2:16129.
  18. Morrison E, S Newman , HS Bae, Z He, J Zhou, KR Reddy, A Ogram. 2016. Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland. Geoderma. 268:119-127.
  19. Penton, C.R., C. Yang, L. Wu, Q. Wang, J. Zhang, F. Liu, Y. Qin, Y. Deng, C. L Hemme, T. Zheng, E. A.G. Schuur, J. M. Tiedje, and J.-Z. Zhou. 2016. NifH- Harboring Bacterial Community Composition Across an Alaskan Permafrost Thaw Gradient. Front. Microbiol. 7:1894. doi: 10.3389/fmicb.2016.01894.
  20. Qiu D, M Xie, J Dai, W An, H Wei, C Tian, ML Kempher, A Zhou, Z He, B Gu and J Zhou. 2016. Differential regulation of the two ferrochelatase paralogues in Shewanella loihica PV-4 in response to environmental stresses. Appl Environ Microbiol 82:5077-5088.
  21. Shen C, Y Shi, Y Ni, Y Deng, J Van Nostrand, Z He, J Zhou, and H Chu. 2016. Dramatic increases of soil microbial functional gene diversity at the treeline ecotone of Changbai Mountain. Front. Microbiol. doi.org/10.3389/fmicb.2016.01184.
  22. Shi S, EE Nuccio , ZJ Shi, Z He, J Zhou, and MK Firestone. 2016. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecol Lett, 19: 926–936.
  23. Sun Y, Y Shen, P Liang, J Zhou, Y Yang, and X Huang. 2016. Multiple antibiotic resistance genes distribution in ten large-scale membrane bioreactors for municipal wastewater treatment. Bioresouce Technol 222:100-106.
  24. Trivedi P, M Delgado-Baquerizo, C Trivedi, H Hu, IC Anderson, TC Jeffries, J Zhou, and BK Singh. 2016. Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships. ISME J. 10:2593-2604.
  25. Tu Q, Y Deng, Q Yan, L Shen, L Lin, Z He, L Wu, JD Van Nostrand, V Buzzard, S Michaletz, B Enquist, M Weiser, M Kaspari, R Waide, J Brown, and J Zhou. 2016. Biogeographic Patterns of Soil Diazotrophic Communities across Six Forests in the North America. Mol Ecol. 25:2937-2948.
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  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
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  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.
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  45. 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 Nickase. Appl. Environ. Microbiol. 81:4423–4431.
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  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 Bank. Geobiology, 12: 231-249.
  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 Gradient, Genomics 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-ecosystem. ISME J 8:714-726.
  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 mutualism. Proc Nat Acad Sci USA. 111(4):14822-14827.
  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 prairie. PLosOne, 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 spill. Front. Microbiol., 5:205. Supplementary Data: Microarray Data (xlsx)
  14. Kuramae, E.E., J. Z. Zhou, G. A. Kowalchuk, and J. A. van Veen. 2014. Soil-borne microbial functional structure across different land uses. Scientific 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.
  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 rhizosphere. PlosOne, DOI: 10.1371/journal.pone.0112609, 9(11):e112609
  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.
  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 alleviation. Biotechnol Biofuels., 7:25. DOI: 10.1186/1754-6834-7-25.
  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 Switchover. Water Res., 54:137-48
  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 sites. Sci 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 metagenomics. Appl. Environ. Microbiol. 80: 1777-1786.
  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 communities. Mol. Ecol. 23:2988-2999. Supplementary Data: Microarray data (xlsx)
  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 insights. J. Bacteriol. 96: 2210-2215
  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 functions. Environ. Microbiol. 16(8):2408-2402.
  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 treatment, Water Research, 56: 162-171.
  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)
  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 Microbiomes. PLoSOne, 9: e90546. doi:10.1371/journal.pone.0090546. Supplementary data: HumiChip data (zip)
  30. Tu, Q., Z. He, and J.-Z. Zhou. 2014. Strain/Species identification in metagenomes using genome-specific markers. Nucl. Acid Res., 42: E67-E67 (Editor picks by Genomeweb)
  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)
  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.
  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 grasslands. Nature Comm. 5:4799. DOI: 10.1038/ncomms5799.
  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
  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.
  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.
  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.
  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 Control. Appl. Environ. Microbiol. 80: 1544-1552. (Review)
  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.
  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)
  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 grassland, ISME J, 8: 430-440
  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 process. J 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 reclamation, J Haz Mat. 269:56-67.
  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 Acidobacteria. J Environ Sci. 26(8):1717-1724.
  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 types. PLoS One, 9: e93773. doi:10.1371/journal.pone.0093773.
  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 supernatant. Water Res. 67:345-354.
  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.
  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, http://www.pnas.org/site/media/current.xhtml#processes) (Also Editor picks by Genomeweb).
  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 ecologists. Front 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.
  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)
  4. Deng Y., Yang Y., He Z., Zhou J. 2013. Molecular ecological network of microbial communities. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). 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
  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.
  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 (www.springerreference.com). 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. Soil microbial community responses to elevated CO2 and O3 in a soybean agroecosystem. ISME J, 8: 714-726, doi:10.1038/ismej.2013.177.
  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.
  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)
  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.
  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.
  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
  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.
  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.
  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.
  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.
  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.
  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.
  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: IN PRESS. DOI: 10.1371/journal.pone.0083909
  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.
  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
  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.
  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
  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: . DOI: 10.1186/1471-2180-13-124
  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.
  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)
  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.
  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.
  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.
  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. doi.org/10.1016/j.watres.2013.08.003. Supplementary Data: Microarray Data (xlsx)
  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.
  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)
  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.
  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 effort
  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.
  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.
  2. Carter, M. Q., K. Xue, M. T. Brandl, F.F. Liu, J. W. Louie, L.Y. Wu, and J.-Z. Zhou. 2012. Interactions between enterohemorrhagic Escherichia coli and spinach-associated microbiota during the biofilm formation: A GeoChip-based metagenomic study, PLoSOne, 7: e44186 DOI: 10.1371/journal.pone.0044186 Supplementary Data: Microarray Data (xls)
  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.
  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.
  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)
  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.
  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)
  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
  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)
  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, http://ec.europa.eu/environment/integration/research/research_alert_en.htm, 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.
  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.
  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.
  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
  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
  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
  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. Doi.org/10.1016/j.soilbio.2012.03.007.
  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.
  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.
  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.
  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.
  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.
  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.
  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, 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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)
  15. 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.
  16. 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.
  17. 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)
  18. 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)
  19. 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.
  20. 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.
  21. 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)
  22. 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)
  23. 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)
  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.
  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).
  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.
  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.
  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.
  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, http://www.the-scientist.com/blog/display/57342/) 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).
  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).
  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).
  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).
  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.
  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).
  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.
  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.
  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).
  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.
  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.
  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.
  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.
  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.
  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
  22. Zhou, J.-Z., 2009. Predictive Microbial Ecology. Microb. Biotechnol. 2: 154–156
  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.
  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.
  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.
  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.
  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).
  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.
  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. 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.
  17. 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.
  18. 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.
  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: (http://www.nature.com/ismej/press_releases/index.html) (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).
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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 (*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 Sym-posium 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.
  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.
  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. (Listed as one of the top 20 papers most requested in 2005 by AEM).
  8. Hu, S. X. Chen, C. Tu, F. Louws, J.-Z. Zhou, D. Shuew. 2005. High soil microbial diversity correlates with pathogen invasion but suppresses pathogen activity. Phytopathology, 95: S45-S45.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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)
  14. 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.
  15. 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.
  16. 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.
  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). http://onlinelibrary.wiley.com/book/10.1002/0471647527
  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).
  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.
  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.
  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.
  34. Zhou, J.-Z., and C.. Chen. 1987. Quantitative measurement of selectivity of predator for prey. Acta Ecologia Sinica, 7: 50-56.
  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.
  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.
  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.