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One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation.

Chen H, Yang ZK, Yip D, Morris RH, Lebreux SJ, Cregger MA, Klingeman DM, Hui D, Hettich RL, Wilhelm SW, Wang G, Löffler FE, Schadt CW.

PLoS One. 2019 Jun 18;14(6):e0211310. doi: 10.1371/journal.pone.0211310. eCollection 2019.


Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin.

Veach AM, Morris R, Yip DZ, Yang ZK, Engle NL, Cregger MA, Tschaplinski TJ, Schadt CW.

Microbiome. 2019 May 18;7(1):76. doi: 10.1186/s40168-019-0668-8.


Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.

Liao HL, Bonito G, Rojas JA, Hameed K, Wu S, Schadt CW, Labbé J, Tuskan GA, Martin F, Grigoriev IV, Vilgalys R.

Mol Plant Microbe Interact. 2019 Jul;32(7):853-864. doi: 10.1094/MPMI-05-18-0133-R. Epub 2019 Jun 10.


Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools.

Ware IM, Van Nuland ME, Schweitzer JA, Yang Z, Schadt CW, Sidak-Loftis LC, Stone NE, Busch JD, Wagner DM, Bailey JK.

Glob Chang Biol. 2019 Jan 18. doi: 10.1111/gcb.14553. [Epub ahead of print]


Methane emissions from tree stems: a new frontier in the global carbon cycle.

Barba J, Bradford MA, Brewer PE, Bruhn D, Covey K, van Haren J, Megonigal JP, Mikkelsen TN, Pangala SR, Pihlatie M, Poulter B, Rivas-Ubach A, Schadt CW, Terazawa K, Warner DL, Zhang Z, Vargas R.

New Phytol. 2019 Apr;222(1):18-28. doi: 10.1111/nph.15582. Epub 2018 Dec 18.


Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism.

Higgins SA, Schadt CW, Matheny PB, Löffler FE.

Genome Biol Evol. 2018 Sep 1;10(9):2474-2489. doi: 10.1093/gbe/evy187.


Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides).

Yip DZ, Veach AM, Yang ZK, Cregger MA, Schadt CW.

New Phytol. 2019 Apr;222(1):115-121. doi: 10.1111/nph.15346. Epub 2018 Jul 6.


Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe.

Dai Z, Su W, Chen H, Barberán A, Zhao H, Yu M, Yu L, Brookes PC, Schadt CW, Chang SX, Xu J.

Glob Chang Biol. 2018 Aug;24(8):3452-3461. doi: 10.1111/gcb.14163. Epub 2018 Apr 25.


Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks.

Karpinets TV, Gopalakrishnan V, Wargo J, Futreal AP, Schadt CW, Zhang J.

Front Microbiol. 2018 Mar 7;9:297. doi: 10.3389/fmicb.2018.00297. eCollection 2018.


The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.

Cregger MA, Veach AM, Yang ZK, Crouch MJ, Vilgalys R, Tuskan GA, Schadt CW.

Microbiome. 2018 Feb 12;6(1):31. doi: 10.1186/s40168-018-0413-8.


Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome.

Timm CM, Carter KR, Carrell AA, Jun SR, Jawdy SS, Vélez JM, Gunter LE, Yang Z, Nookaew I, Engle NL, Lu TS, Schadt CW, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Pelletier DA, Weston DJ.

mSystems. 2018 Jan 23;3(1). pii: e00070-17. doi: 10.1128/mSystems.00070-17. eCollection 2018 Jan-Feb.


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.


Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota.

Warren MJ, Lin X, Gaby JC, Kretz CB, Kolton M, Morton PL, Pett-Ridge J, Weston DJ, Schadt CW, Kostka JE, Glass JB.

Appl Environ Microbiol. 2017 Aug 17;83(17). pii: e01174-17. doi: 10.1128/AEM.01174-17. Print 2017 Sep 1.


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.


Stability of peatland carbon to rising temperatures.

Wilson RM, Hopple AM, Tfaily MM, Sebestyen SD, Schadt CW, Pfeifer-Meister L, Medvedeff C, McFarlane KJ, Kostka JE, Kolton M, Kolka RK, Kluber LA, Keller JK, Guilderson TP, Griffiths NA, Chanton JP, Bridgham SD, Hanson PJ.

Nat Commun. 2016 Dec 13;7:13723. doi: 10.1038/ncomms13723.


Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.

Utturkar SM, Cude WN, Robeson MS Jr, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA.

Appl Environ Microbiol. 2016 Aug 30;82(18):5698-708. doi: 10.1128/AEM.01285-16. Print 2016 Sep 15.


A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization.

Bible AN, Fletcher SJ, Pelletier DA, Schadt CW, Jawdy SS, Weston DJ, Engle NL, Tschaplinski T, Masyuko R, Polisetti S, Bohn PW, Coutinho TA, Doktycz MJ, Morrell-Falvey JL.

Front Microbiol. 2016 Apr 18;7:491. doi: 10.3389/fmicb.2016.00491. eCollection 2016.


Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils.

Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE.

Appl Environ Microbiol. 2016 May 2;82(10):2919-2928. doi: 10.1128/AEM.00243-16. Print 2016 May 15.


Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere.

Klingeman DM, Utturkar S, Lu TY, Schadt CW, Pelletier DA, Brown SD.

Genome Announc. 2015 Nov 12;3(6). pii: e01344-15. doi: 10.1128/genomeA.01344-15.


Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TY, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA.

Front Microbiol. 2015 Oct 14;6:1118. doi: 10.3389/fmicb.2015.01118. eCollection 2015.


Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW.

Appl Environ Microbiol. 2015 Oct 30;82(1):375-83. doi: 10.1128/AEM.02612-15. Print 2016 Jan 1.


Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities.

Deng Y, He Z, Xiong J, Yu H, Xu M, Hobbie SE, Reich PB, Schadt CW, Kent A, Pendall E, Wallenstein M, Zhou J.

Glob Chang Biol. 2016 Feb;22(2):957-64. doi: 10.1111/gcb.13098. Epub 2015 Oct 23.


PanFP: pangenome-based functional profiles for microbial communities.

Jun SR, Robeson MS, Hauser LJ, Schadt CW, Gorin AA.

BMC Res Notes. 2015 Sep 26;8:479. doi: 10.1186/s13104-015-1462-8.


Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation.

Deng Y, Zhang P, Qin Y, Tu Q, Yang Y, He Z, Schadt CW, Zhou J.

Environ Microbiol. 2016 Jan;18(1):205-18. doi: 10.1111/1462-2920.12981. Epub 2015 Aug 11.


FUNGAL BIOGEOGRAPHY. Comment on "Global diversity and geography of soil fungi".

Schadt CW, Rosling A.

Science. 2015 Jun 26;348(6242):1438. doi: 10.1126/science.aaa4269.


Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

Zhang P, Wu WM, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt CW, Watson D, Jardine P, Criddle CS, Brooks S, Marsh TL, Tiedje JM, Arkin AP, Zhou J.

Appl Environ Microbiol. 2015 Jun 15;81(12):4164-72. doi: 10.1128/AEM.00043-15. Epub 2015 Apr 10.


Towards a holistic understanding of the beneficial interactions across the Populus microbiome.

Hacquard S, Schadt CW.

New Phytol. 2015 Mar;205(4):1424-30. doi: 10.1111/nph.13133. Epub 2014 Nov 24. Review.


Microbial dormancy improves development and experimental validation of ecosystem model.

Wang G, Jagadamma S, Mayes MA, Schadt CW, Steinweg JM, Gu L, Post WM.

ISME J. 2015 Jan;9(1):226-37. doi: 10.1038/ismej.2014.120. Epub 2014 Jul 11.


Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD.

Bioinformatics. 2014 Oct;30(19):2709-16. doi: 10.1093/bioinformatics/btu391. Epub 2014 Jun 14.


Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants.

Bonito G, Reynolds H, Robeson MS 2nd, Nelson J, Hodkinson BP, Tuskan G, Schadt CW, Vilgalys R.

Mol Ecol. 2014 Jul;23(13):3356-70. doi: 10.1111/mec.12821.


Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA.

Lin X, Tfaily MM, Steinweg JM, Chanton P, Esson K, Yang ZK, Chanton JP, Cooper W, Schadt CW, Kostka JE.

Appl Environ Microbiol. 2014 Jun;80(11):3518-30. doi: 10.1128/AEM.00205-14. Epub 2014 Mar 28.


Representation of dormant and active microbial dynamics for ecosystem modeling.

Wang G, Mayes MA, Gu L, Schadt CW.

PLoS One. 2014 Feb 18;9(2):e89252. doi: 10.1371/journal.pone.0089252. eCollection 2014.


Watershed-scale fungal community characterization along a pH gradient in a subsurface environment cocontaminated with uranium and nitrate.

Jasrotia P, Green SJ, Canion A, Overholt WA, Prakash O, Wafula D, Hubbard D, Watson DB, Schadt CW, Brooks SC, Kostka JE.

Appl Environ Microbiol. 2014 Mar;80(6):1810-20. doi: 10.1128/AEM.03423-13. Epub 2014 Jan 3.


A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.

Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, Podar M, Schadt CW.

PLoS One. 2013 Oct 16;8(10):e76382. doi: 10.1371/journal.pone.0076382. eCollection 2013.


U(VI) bioreduction with emulsified vegetable oil as the electron donor--model application to a field test.

Tang G, Watson DB, Wu WM, Schadt CW, Parker JC, Brooks SC.

Environ Sci Technol. 2013 Apr 2;47(7):3218-25. doi: 10.1021/es304643h. Epub 2013 Mar 14.


U(VI) bioreduction with emulsified vegetable oil as the electron donor--microcosm tests and model development.

Tang G, Wu WM, Watson DB, Parker JC, Schadt CW, Shi X, Brooks SC.

Environ Sci Technol. 2013 Apr 2;47(7):3209-17. doi: 10.1021/es304641b. Epub 2013 Feb 28.


Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M.

Environ Microbiol. 2013 Jun;15(6):1882-99. doi: 10.1111/1462-2920.12086. Epub 2013 Feb 6.


Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 Nov;194(21):5991-3. doi: 10.1128/JB.01243-12.


Response of the soil microbial community to changes in precipitation in a semiarid ecosystem.

Cregger MA, Schadt CW, McDowell NG, Pockman WT, Classen AT.

Appl Environ Microbiol. 2012 Dec;78(24):8587-94. doi: 10.1128/AEM.02050-12. Epub 2012 Sep 28.


Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization.

Sullivan TS, Gottel NR, Basta N, Jardine PM, Schadt CW.

Appl Environ Microbiol. 2012 Sep;78(17):6078-86. doi: 10.1128/AEM.01091-12. Epub 2012 Jun 22.


Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides.

Brown SD, Klingeman DM, Lu TY, Johnson CM, Utturkar SM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 May;194(9):2383-4. doi: 10.1128/JB.00198-12.


Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis, and fitness.

Weston DJ, Pelletier DA, Morrell-Falvey JL, Tschaplinski TJ, Jawdy SS, Lu TY, Allen SM, Melton SJ, Martin MZ, Schadt CW, Karve AA, Chen JG, Yang X, Doktycz MJ, Tuskan GA.

Mol Plant Microbe Interact. 2012 Jun;25(6):765-78. doi: 10.1094/MPMI-09-11-0253.


Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp.

Mosher JJ, Phelps TJ, Podar M, Hurt RA Jr, Campbell JH, Drake MM, Moberly JG, Schadt CW, Brown SD, Hazen TC, Arkin AP, Palumbo AV, Faybishenko BA, Elias DA.

Appl Environ Microbiol. 2012 Apr;78(7):2082-91. doi: 10.1128/AEM.07165-11. Epub 2012 Jan 20.


Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.

Dunbar J, Eichorst SA, Gallegos-Graves LV, Silva S, Xie G, Hengartner NW, Evans RD, Hungate BA, Jackson RB, Megonigal JP, Schadt CW, Vilgalys R, Zak DR, Kuske CR.

Environ Microbiol. 2012 May;14(5):1145-58. doi: 10.1111/j.1462-2920.2011.02695.x. Epub 2012 Jan 20.


Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations.

Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M Jr, Liao JC, Schadt CW, Guss AM, Yang Y, Graham DE.

Biotechnol Biofuels. 2012 Jan 4;5(1):2. doi: 10.1186/1754-6834-5-2.


Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

Green SJ, Prakash O, Jasrotia P, Overholt WA, Cardenas E, Hubbard D, Tiedje JM, Watson DB, Schadt CW, Brooks SC, Kostka JE.

Appl Environ Microbiol. 2012 Feb;78(4):1039-47. doi: 10.1128/AEM.06435-11. Epub 2011 Dec 16.


Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.

Gihring TM, Green SJ, Schadt CW.

Environ Microbiol. 2012 Feb;14(2):285-90. doi: 10.1111/j.1462-2920.2011.02550.x. Epub 2011 Sep 19.


Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.

Hodkinson BP, Gottel NR, Schadt CW, Lutzoni F.

Environ Microbiol. 2012 Jan;14(1):147-61. doi: 10.1111/j.1462-2920.2011.02560.x. Epub 2011 Sep 12.


Responses of soil cellulolytic fungal communities to elevated atmospheric CO₂ are complex and variable across five ecosystems.

Weber CF, Zak DR, Hungate BA, Jackson RB, Vilgalys R, Evans RD, Schadt CW, Megonigal JP, Kuske CR.

Environ Microbiol. 2011 Oct;13(10):2778-93. doi: 10.1111/j.1462-2920.2011.02548.x. Epub 2011 Sep 1.


A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer.

Gihring TM, Zhang G, Brandt CC, Brooks SC, Campbell JH, Carroll S, Criddle CS, Green SJ, Jardine P, Kostka JE, Lowe K, Mehlhorn TL, Overholt W, Watson DB, Yang Z, Wu WM, Schadt CW.

Appl Environ Microbiol. 2011 Sep;77(17):5955-65. doi: 10.1128/AEM.00220-11. Epub 2011 Jul 15.

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