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Adaptive Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River Sediment.

Song D, Chen X, Xu M, Hai R, Zhou A, Tian R, Van Nostrand JD, Kempher ML, Guo J, Sun G, Zhou J.

Front Microbiol. 2019 Oct 2;10:2263. doi: 10.3389/fmicb.2019.02263. eCollection 2019.


Author Correction: Continental scale structuring of forest and soil diversity via functional traits.

Buzzard V, Michaletz ST, Deng Y, He Z, Ning D, Shen L, Tu Q, Van Nostrand JD, Voordeckers JW, Wang J, Weiser MD, Kaspari M, Waide RB, Zhou J, Enquist BJ.

Nat Ecol Evol. 2019 Oct 3. doi: 10.1038/s41559-019-1014-z. [Epub ahead of print]


Continental scale structuring of forest and soil diversity via functional traits.

Buzzard V, Michaletz ST, Deng Y, He Z, Ning D, Shen L, Tu Q, Van Nostrand JD, Voordeckers JW, Wang J, Weiser MD, Kaspari M, Waide RB, Zhou J, Enquist BJ.

Nat Ecol Evol. 2019 Sep;3(9):1298-1308. doi: 10.1038/s41559-019-0954-7. Epub 2019 Aug 19. Erratum in: Nat Ecol Evol. 2019 Oct 3;:.


Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus.

Li Y, Wang K, Zhang B, Tu Q, Yao Y, Cui B, Ren B, He J, Shen X, Van Nostrand JD, Zhou J, Shi W, Xiao L, Lu C, Zhou X.

Int J Oral Sci. 2019 Jul 2;11(2):13. doi: 10.1038/s41368-019-0045-2.


Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.

Shi Z, Yin H, Van Nostrand JD, Voordeckers JW, Tu Q, Deng Y, Yuan M, Zhou A, Zhang P, Xiao N, Ning D, He Z, Wu L, Zhou J.

mSystems. 2019 Jun 18;4(4). pii: e00296-19. doi: 10.1128/mSystems.00296-19.


Global diversity and biogeography of bacterial communities in wastewater treatment plants.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A; Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J.

Nat Microbiol. 2019 Jul;4(7):1183-1195. doi: 10.1038/s41564-019-0426-5. Epub 2019 May 13.


Taxonomic and functional responses of soil microbial communities to slag-based fertilizer amendment in rice cropping systems.

Das S, Gwon HS, Khan MI, Van Nostrand JD, Alam MA, Kim PJ.

Environ Int. 2019 Jun;127:531-539. doi: 10.1016/j.envint.2019.04.012. Epub 2019 Apr 11.


Climate warming accelerates temporal scaling of grassland soil microbial biodiversity.

Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Qiu G, Liu X, Luo Y, Tiedje JM, Yang Y, Zhou J.

Nat Ecol Evol. 2019 Apr;3(4):612-619. doi: 10.1038/s41559-019-0848-8. Epub 2019 Mar 25.


Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.

Feng J, Penton CR, He Z, Van Nostrand JD, Yuan MM, Wu L, Wang C, Qin Y, Shi ZJ, Guo X, Schuur EAG, Luo Y, Bracho R, Konstantinidis KT, Cole JR, Tiedje JM, Yang Y, Zhou J.

MBio. 2019 Feb 26;10(1). pii: e02521-18. doi: 10.1128/mBio.02521-18.


Microbial functional traits are sensitive indicators of mild disturbance by lamb grazing.

Ma X, Zhang Q, Zheng M, Gao Y, Yuan T, Hale L, Van Nostrand JD, Zhou J, Wan S, Yang Y.

ISME J. 2019 May;13(5):1370-1373. doi: 10.1038/s41396-019-0354-7. Epub 2019 Jan 30.


Elevated CO2 and Warming Altered Grassland Microbial Communities in Soil Top-Layers.

Yu H, Deng Y, He Z, Van Nostrand JD, Wang S, Jin D, Wang A, Wu L, Wang D, Tai X, Zhou J.

Front Microbiol. 2018 Aug 14;9:1790. doi: 10.3389/fmicb.2018.01790. eCollection 2018.


Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass.

Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM, Zhou J.

Front Microbiol. 2018 May 31;9:954. doi: 10.3389/fmicb.2018.00954. eCollection 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.

Dignam BEA, O'Callaghan M, Condron LM, Kowalchuk GA, Van Nostrand JD, Zhou J, Wakelin SA.

PLoS One. 2018 May 7;13(5):e0196581. doi: 10.1371/journal.pone.0196581. eCollection 2018.


Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition.

Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin AP, Elias DA.

PLoS One. 2018 Mar 20;13(3):e0194663. doi: 10.1371/journal.pone.0194663. eCollection 2018.


Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China.

Vishnivetskaya TA, Hu H, Van Nostrand JD, Wymore AM, Xu X, Qiu G, Feng X, Zhou J, Brown SD, Brandt CC, Podar M, Gu B, Elias DA.

Environ Sci Process Impacts. 2018 Apr 25;20(4):673-685. doi: 10.1039/c7em00558j.


Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J.

MBio. 2018 Feb 20;9(1). pii: e02435-17. doi: 10.1128/mBio.02435-17.


Correction: Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations.

Gu Y, Van Nostrand JD, Wu L, He Z, Qin Y, Zhao FJ, Zhou J.

PLoS One. 2017 Dec 7;12(12):e0189656. doi: 10.1371/journal.pone.0189656. eCollection 2017.


Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

Zhang Y, Yang Q, Ling J, Van Nostrand JD, Shi Z, Zhou J, Dong J.

Front Microbiol. 2017 Oct 18;8:2032. doi: 10.3389/fmicb.2017.02032. eCollection 2017.


Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers.

Yu H, He Z, Wang A, Xie J, Wu L, Van Nostrand JD, Jin D, Shao Z, Schadt CW, Zhou J, Deng Y.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01694-17. doi: 10.1128/AEM.01694-17. Print 2018 Jan 1.


Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment.

Yang Z, Yang S, Van Nostrand JD, Zhou J, Fang W, Qi Q, Liu Y, Wullschleger SD, Liang L, Graham DE, Yang Y, Gu B.

Front Microbiol. 2017 Sep 19;8:1741. doi: 10.3389/fmicb.2017.01741. eCollection 2017.


Cas9 Nickase-Assisted RNA Repression Enables Stable and Efficient Manipulation of Essential Metabolic Genes in Clostridium cellulolyticum.

Xu T, Li Y, He Z, Van Nostrand JD, Zhou J.

Front Microbiol. 2017 Sep 7;8:1744. doi: 10.3389/fmicb.2017.01744. eCollection 2017.


Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts.

He J, Tu Q, Ge Y, Qin Y, Cui B, Hu X, Wang Y, Deng Y, Wang K, Van Nostrand JD, Li J, Zhou J, Li Y, Zhou X.

Microb Ecol. 2018 Feb;75(2):543-554. doi: 10.1007/s00248-017-1056-1. Epub 2017 Sep 20.


Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence.

Colin Y, Nicolitch O, Van Nostrand JD, Zhou JZ, Turpault MP, Uroz S.

Sci Rep. 2017 Aug 29;7(1):9604. doi: 10.1038/s41598-017-07639-1.


Contradictory effects of silver nanoparticles on activated sludge wastewater treatment.

Sheng Z, Van Nostrand JD, Zhou J, Liu Y.

J Hazard Mater. 2018 Jan 5;341:448-456. doi: 10.1016/j.jhazmat.2017.07.051. Epub 2017 Aug 2.


Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

Yuan MM, Zhang J, Xue K, Wu L, Deng Y, Deng J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EAG, Konstantinidis KT, Penton CR, Cole JR, Tiedje JM, Luo Y, Zhou J.

Glob Chang Biol. 2018 Jan;24(1):297-307. doi: 10.1111/gcb.13820. Epub 2017 Sep 1.


Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment.

Wang Y, Zhang R, He Z, Van Nostrand JD, Zheng Q, Zhou J, Jiao N.

Front Microbiol. 2017 Jun 21;8:1153. doi: 10.3389/fmicb.2017.01153. eCollection 2017.


Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

Yan Z, He Y, Cai H, Van Nostrand JD, He Z, Zhou J, Krumholz LR, Jiang HL.

Environ Sci Technol. 2017 Aug 1;51(15):8519-8529. doi: 10.1021/acs.est.7b00209. Epub 2017 Jul 14.


Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

Li P, Jiang Z, Wang Y, Deng Y, Van Nostrand JD, Yuan T, Liu H, Wei D, Zhou J.

Water Res. 2017 Oct 15;123:268-276. doi: 10.1016/j.watres.2017.06.053. Epub 2017 Jun 21.


Correspondence: Reply to 'Analytical flaws in a continental-scale forest soil microbial diversity study'.

Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, Qin Y, Xue K, Wu L, He Z, Voordeckers JW, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Yang Y, Brown JH.

Nat Commun. 2017 Jun 6;8:15583. doi: 10.1038/ncomms15583. No abstract available.


Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling.

Wu L, Yang Y, Wang S, Yue H, Lin Q, Hu Y, He Z, Van Nostrand JD, Hale L, Li X, Gilbert JA, Zhou J.

ISME J. 2017 Sep;11(9):2102-2111. doi: 10.1038/ismej.2017.75. Epub 2017 May 23.


Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

Wen C, Wu L, Qin Y, Van Nostrand JD, Ning D, Sun B, Xue K, Liu F, Deng Y, Liang Y, Zhou J.

PLoS One. 2017 Apr 28;12(4):e0176716. doi: 10.1371/journal.pone.0176716. eCollection 2017.


Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China).

Yan Q, Stegen JC, Yu Y, Deng Y, Li X, Wu S, Dai L, Zhang X, Li J, Wang C, Ni J, Li X, Hu H, Xiao F, Feng W, Ning D, He Z, Van Nostrand JD, Wu L, Zhou J.

Mol Ecol. 2017 Jul;26(14):3839-3850. doi: 10.1111/mec.14151. Epub 2017 May 21.


Warming enhances old organic carbon decomposition through altering functional microbial communities.

Cheng L, Zhang N, Yuan M, Xiao J, Qin Y, Deng Y, Tu Q, Xue K, Van Nostrand JD, Wu L, He Z, Zhou X, Leigh MB, Konstantinidis KT, Schuur EA, Luo Y, Tiedje JM, Zhou J.

ISME J. 2017 Aug;11(8):1825-1835. doi: 10.1038/ismej.2017.48. Epub 2017 Apr 21.


Elucidation of the methanogenic potential from coalbed microbial communities amended with volatile fatty acids.

Lyles CN, Parisi VA, Beasley WH, Van Nostrand JD, Zhou J, Suflita JM.

FEMS Microbiol Ecol. 2017 Apr 1;93(4). doi: 10.1093/femsec/fix040.


Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer.

Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J.

Environ Sci Technol. 2017 Apr 4;51(7):3609-3620. doi: 10.1021/acs.est.6b02980. Epub 2017 Mar 16.


The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea.

Zhang Y, Yang Q, Ling J, Van Nostrand JD, Shi Z, Zhou J, Dong J.

Front Microbiol. 2016 Nov 22;7:1870. eCollection 2016.


Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica.

Wei ST, Lacap-Bugler DC, Lau MC, Caruso T, Rao S, de Los Rios A, Archer SK, Chiu JM, Higgins C, Van Nostrand JD, Zhou J, Hopkins DW, Pointing SB.

Front Microbiol. 2016 Oct 20;7:1642. eCollection 2016.


Anaerobic Disposal of Arsenic-Bearing Wastes Results in Low Microbially Mediated Arsenic Volatilization.

Webster TM, Reddy RR, Tan JY, Van Nostrand JD, Zhou J, Hayes KF, Raskin L.

Environ Sci Technol. 2016 Oct 18;50(20):10951-10959. doi: 10.1021/acs.est.6b02286. Epub 2016 Oct 7.


A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom.

Yang C, Li Y, Zhou Y, Lei X, Zheng W, Tian Y, Van Nostrand JD, He Z, Wu L, Zhou J, Zheng T.

Sci Rep. 2016 Oct 5;6:34645. doi: 10.1038/srep34645.


The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

Niu J, Deng J, Xiao Y, He Z, Zhang X, Van Nostrand JD, Liang Y, Deng Y, Liu X, Yin H.

Sci Rep. 2016 Oct 4;6:34744. doi: 10.1038/srep34744.


Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming.

Xue K, Yuan MM, Xie J, Li D, Qin Y, Hale LE, Wu L, Deng Y, He Z, Van Nostrand JD, Luo Y, Tiedje JM, Zhou J.

MBio. 2016 Sep 27;7(5). pii: e00976-16. doi: 10.1128/mBio.00976-16.


Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

Shen C, Shi Y, Ni Y, Deng Y, Van Nostrand JD, He Z, Zhou J, Chu H.

Front Microbiol. 2016 Jul 29;7:1184. doi: 10.3389/fmicb.2016.01184. eCollection 2016.


Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah.

Lindsay MR, Anderson C, Fox N, Scofield G, Allen J, Anderson E, Bueter L, Poudel S, Sutherland K, Munson-McGee JH, Van Nostrand JD, Zhou J, Spear JR, Baxter BK, Lageson DR, Boyd ES.

Geobiology. 2017 Jan;15(1):131-145. doi: 10.1111/gbi.12201. Epub 2016 Jul 14.


Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning.

Xue K, Xie J, Zhou A, Liu F, Li D, Wu L, Deng Y, He Z, Van Nostrand JD, Luo Y, Zhou J.

Front Microbiol. 2016 May 6;7:668. doi: 10.3389/fmicb.2016.00668. eCollection 2016.


Environmental filtering decreases with fish development for the assembly of gut microbiota.

Yan Q, Li J, Yu Y, Wang J, He Z, Van Nostrand JD, Kempher ML, Wu L, Wang Y, Liao L, Li X, Wu S, Ni J, Wang C, Zhou J.

Environ Microbiol. 2016 Dec;18(12):4739-4754. doi: 10.1111/1462-2920.13365. Epub 2016 Jun 8.


Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring.

Jiang Z, Li P, Van Nostrand JD, Zhang P, Zhou J, Wang Y, Dai X, Zhang R, Jiang D, Wang Y.

Sci Rep. 2016 Apr 29;6:25262. doi: 10.1038/srep25262.


Biogeographic patterns of soil diazotrophic communities across six forests in North America.

Tu Q, Deng Y, Yan Q, Shen L, Lin L, He Z, Wu L, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide RB, Brown JH, Zhou J.

Mol Ecol. 2016 Jun;25(12):2937-48. doi: 10.1111/mec.13651. Epub 2016 May 21. Erratum in: Mol Ecol. 2017 Apr;26(8):2405.


Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.

Hemme CL, Green SJ, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutschbauer AM, Van Nostrand JD, Wu L, He Z, Jordan IK, Hazen TC, Arkin AP, Kostka JE, Zhou J.

MBio. 2016 Apr 5;7(2):e02234-15. doi: 10.1128/mBio.02234-15.


Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus.

Wang K, Lu W, Tu Q, Ge Y, He J, Zhou Y, Gou Y, Van Nostrand JD, Qin Y, Li J, Zhou J, Li Y, Xiao L, Zhou X.

Sci Rep. 2016 Mar 10;6:22943. doi: 10.1038/srep22943.


Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip.

Van Nostrand JD, Yin H, Wu L, Yuan T, Zhou J.

Methods Mol Biol. 2016;1399:183-96. doi: 10.1007/978-1-4939-3369-3_11.


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