Publications

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JOURNAL PUBLICATIONS

2015

  1. Deng, Y, P Zhang, Y Qin, Q Tu, Y Yang, Z He, CW Schadt and J Zhou. (2015). Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environmental Microbiology. In Press
  2. Hacquard, S and CW Schadt (2015). Towards a holistic understanding of the beneficial interactions across the Populus microbiome. New Phytologist, 205(4): 1424-1430.
  3. Naujokas, MF, NT Basta, Z Cheng, GM Hettiarachchi, M Maddaloni, CW Schadt, KG Scheckel, C Attanayake and H Henry. (2015). Bioavailability-based In Situ Remediation to Meet Future Lead (Pb) Standards in Urban Soils and Gardens. Environmental Science & Technology. 49(15):8948–8958
  4. Schadt, CW and A Rosling. (2015). Comment on “Global diversity and geography of soil fungi”. Science. 348(6242): 1438-1438.
  5. Wang, G, S Jagadamma, MA Mayes, CW Schadt, JM Steinweg, L Gu and WM Post. (2015). Microbial dormancy improves development and experimental validation of ecosystem model. ISME Journal. 9: 226-237.
  6. Zhang, P, WM Wu, JD Van Nostrand, Y Deng, Z He, T Gihring, G Zhang, CW Schadt, D Watson, P Jardine, CS Criddle, S Brooks, TL Marsh, JM Tiedje, AP Arkin and J Zhou. (2015). Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U (VI) reduction. Applied and Environmental Microbiology. 81(12): 4164-4172.

2014

  1. Bonito, G, H Reynolds, M Robeson, J Nelson, B Hodkinson, G Tuskan, CW Schadt and R Vilgalys. (2014). Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants.  Molecular Ecology: 23(13): 3356-3370.
  2. Jastoria, P, SJ Green, A Canion, WA Overholt, O Prakash, D Wafula, D Hubbard, DB Watson, CW Schadt, SC Brooks and JE Kostka. (2014). Watershed scale fungal community characterization along a pH gradient in a subsurface environment co-contaminated with uranium and nitrate. Applied and Environmental Microbiology, 80:1810-1820.
  3. Lin, X, MM Tfaily, JM Steinweg, P Chanton, K Esson, ZK Yang, JP Chanton, W Cooper, CW Schadt and JE Kostka (2014). Microbial metabolic potential in carbon degradation and nutrient acquisition (N, P) in an ombrotrophic peatland. Applied and Environmental Microbiology, 80:3531-3540.
  4. Lin, X, MM Tfaily, SJ Green, JM Steinweg, P Chanton, A Imvittaya, JP Chanton, W Cooper, CW Schadt and JE Kostka (2014). Microbial community stratification linked to variation in organic matter properties in a boreal peatland. Applied and Environmental Microbiology, 80:3518-3530.
  5. Tfaily, MM, WT Cooper, JE Kostka, PR Chanton, CW Schadt, PJ Hanson, CM Iversen and JP Chanton. (2014). Organic matter transformation in the peat column at Marcell Experimental forest: Humification and vertical stratification. Journal of Geophysical Research: Biogeosciences, 119:661-675.
  6. Utturkar, SM, DM Klingeman, ML Land, CW Schadt, MJ Doktycz, DA Pelletier and SD Brown (2014). Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences. 30(19): 2709-2716.
  7. Wang, G, MA Mayes, L Gu, and CW Schadt. (2014). Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling. PLoS ONE 9:

2013

  1. De Graaff, MA, J Six, J Jastrow, J Phillips, CW Schadt and SD Wullschleger. (2013). Variation in root architecture among switchgrass cultivars impacts root decomposition rates. Soil Biology and Biochemistry 58:198-206
  2. Guevara, G, G Bonito, J Trappe, E Cazares, G Williams, RA Healy, CW Schadt and R Vilgalys. (2013). New North American truffles (Tuber ) species and their ectomycorrhizal associations. Mycologia 105:194–209.
  3. Shakya, M, C Quince, JH Campbell, ZK Yang, CW Schadt and M Podar. (2013). Comparative metagenomic and rRNA microbial diversity characterization using Archaeal and Bacterial synthetic communities. Environmental Microbiology 15:1882-1889
  4. Shakya M, N Gottel, H Castro, ZK Yang, L Gunter, J Labbe, W Muchero, G Bonito, R Vilgalys, G Tuskan, M Podar and CW Schadt. (2013) A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees. PLoS ONE 8:
  5. Tang, GP, W-M Wu, DB Watson, JC Parker, CW Schadt, X Shi, and SC Brooks. (2013). U(VI) Bioreduction with Emulsified Vegetable Oil as the Electron Donor – Microcosm Tests and Model Development. Environmental Science and Technology. 47:3209–3217
  6. Tang, GP, DB Watson, W-M Wu, CW Schadt, JC Parker and SC Brooks. (2013) U(VI) Bioreduction with Emulsified Vegetable Oil as the Electron Donor – Model Application to a Field Test. Environmental Science and Technology. 47:3218–3225
  7. Watson, DB, W Wu, T Mehlhorn, G Tang, J Earles, K Lowe, TM Gihring, G Zhang, J Phillips, MI Boyanov, BP Spalding, CW Schadt, KM Kemner, CS Criddle, PM Jardine and SC Brooks. (2013). In situ bioremediation of uranium with emulsified vegetable oil as the electron donor. Environmental Science &Technology 47:6440-6448.

2012

  1. Brown SD, DM Kingeman, TS Lu, CM Johnson, SM Utturkar, ML Land, CW Schadt, MJ Doktycz and DA Pelletier. (2012). Genome Announcement: Draft genome sequence of Rhizobium sp. strain PDO-076, a bacterium isolated from Populus deltoides. Journal of Bacteriology, 194:2383-2384.
  2. Brown SD, SM Utturkar, DM Klingeman, CM Johnson, M Stanton, ML Land, TY Lu, CW Schadt, MJ Doktycz and DA Pelletier. (2012). Genome Announcement: Twenty One Pseudomonas Genomes and Nineteen Genomes from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides. Journal of Bacteriology 194:5991-5993
  3. Castro HF, AT Classen, EE Austin, KM Crawford and CW Schadt. (2012). Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities. Applied Soil Ecology 61:69-75
  4. Cregger, MA, CW Schadt, NG McDowell, WT Pockman and AT Classen. (2012). Soil microbial community response to precipitation change in a semi-arid ecosystem. Applied and Environmental Microbiology 78:8587-8594
  5. Dunbar J, SA Eichorst, L Gallegos-Graves, S Silva, G Xie, NW Hengartner, RD Evans, BA Hungate, RB Jackson, JP Megonigal, CW Schadt, R Vilgalys, DR Zak, and CR Kuske (2012) Common bacterial responses in six ecosystems exposed to ten years of elevated atmospheric carbon dioxide. Environmental Microbiology 14:1145-1158
  6. Gihring TM, SJ Green and CW Schadt. (2012). Massively-parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environmental Microbiology, 14:285-289
  7. Green SJ, O Prakash, P Jasrotia, W Overholt, EA Cardenas, D Hubbard, J Tiedje, DB Watson, CW Schadt, SC Brooks and JE Kostka. (2012). Denitrifying bacteria in the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Applied and Environmental Microbiology, 78:1039-1047
  8. Hodkinson BP, NR Gottel, CW Schadt, and F Lutzoni. (2012). Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology, 14:147-161.
  9. Li Y, TJ Tshaplinski, NL Engle, CY Hamilton, M Rodriguez Jr., JC Liao, CW Schadt, AM Guss, Y Yang and DE Graham. (2012). Combined inactivation of the Clostridum cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yields from cellulose and switchgrass fermentations. Journal of Biotechnology for Biofuels 5:2-13
  10. Mosher JJ, TJ Phelps, M Podar, RA Hurt, JH Campbell, MM Drake, JG Moberly, CW Schadt, SD Brown, TC Hazen, AV Palumbo, BA Faybishenko and DA Elias. (2012). Microbial Community Succession during Lactate Amendment and Electron-acceptor Limitation Reveals a Predominance of Metal-reducing Pelosinus Applied and Environmental Microbiology 78:2082-2091.
  11. Sullivan, TS, NR Gottel, N Basta, PM Jardine and CW Schadt. (2012). Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb-mineral solubilization. Applied and Environmental Microbiology 78:6078-6086 (Images featured on journal cover, Dec Issue 2012)
  12. Weston DJ, DA Pelletier, JL Morrell-Falvey, TJ Tschaplinski, SJ Jawdy, TY Lu, SM Allen, A Karve, SJ Melton, MZ Martin, CW Schadt, JG Chen, X Yang, MJ Doktycz and G Tuskan. (2012). Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis and fitness. Molecular Plant Microbe Interactions 25:765-778

2011

  1. DeGraaff MA, CW Schadt, K Rula, J Six, JA Schwietzer and AT Classen. (2011). Elevated CO2 and plant species diversity interact to alter root decomposition. Soil Biology and Biochemistry 43:2347-2354.
  2. Garten Jr. CT, DJ Brice, HF Castro, RL Graham, MA Mayes, JR Phillips, WM Post, CW Schadt, SD Wullschleger, DD Tyler, PM Jardine, JD Jastrow, R Matamala, RM Miller, KK Moran, TW Vugteveen, RC Izaurralde, AM Thomson, TO West, JE Amonette, VL Bailey, FB Metting and JL Smith. (2011). Response of “Alamo” switchgrass tissue chemistry and biomass to nitrogen fertilization in West Tennessee, USA. Agriculture Ecosystems and Environment 140: 289-297
  3. Gihring TM, G Zhang, CC Brandt, SC Brooks, JH Campbell, S Carroll, CS Criddle, SJ Green, P Jardine, JE Kostka, K Lowe, TL Mehlhorn, W Overholt, DB Watson, ZK Yang, W-M Wu, and CW Schadt. A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer. Applied and Environmental Microbiology, 77:5955-5965
  4. Gilmour CC, DA Elias, AM Kucken, SD Brown, AV Palumbo, CW Schadt and JD Wall. (2011). The sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation. Applied and Environmental Microbiology, 77:3938–3951
  5. Gottel, NR, HF Castro, M Kerley, ZK Yang, DA Pelletier, M Podar, T Karpinets E Uberbacher, GA Tuskan, R Vilgalys, MJ Doktycz, CW Schadt. (2011). Populus deltoides roots harbor distinct microbial communities within the endosphere and rhizosphere across contrasting soil types. Applied and Environmental Microbiology, 77:5934-5944.
  6. Weber CF, DR Zak, BA Hungate, RB Jackson, R Vilgalys, RD Evans, CW Schadt, JP Megonigal and CR Kuske. (2011). Responses of soil cellulolytic fungal communities to elevated atmospheric CO2 are complex and variable across five ecosystems. Environmental Microbiology, 13:2778-2793

2010

  1. Castro HF, AT Classen, EE Austin, RJ Norby and CW Schadt. (2010) Soil microbial community responses to multiple climate change drivers. Applied and Environmental Microbiology 76:999-1007.
  2. Degraff MA, AT Classen, HF Castro and CW Schadt. (2010) Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates. New Phytologist. 188:1055-1064
  3. Garten Jr, CT Jr., JL Smith, DD Tyler, JE Amonette, VL Bailey, DJ Brice, HF Castro, RL Graham, CA Gunderson, RC Izaurralde, PM Jardine, JD Jastrow, MK Kerley, R Matamala, MA Mayes, FB Metting, RM Miller, KK Moran, WM Post III, RD Sands, CW Schadt, JR Phillips, AM Thomson, T Vugteveen, TO West, and SD Wullschleger. (2010) Intra-annual changes in biomass, carbon, and nitrogen dynamics at 4-year old switchgrass field trials in west Tennessee, USA. Agriculture Ecosystems and Environment 136:177-184.
  4. Hemme CL, H Mouttaki, Y-J Lee, L Goodwin, S Lucas, A Copeland, A Lapidus, T Glavina del Rio, H Tice, E Saunders, T Brettin, JC Detter, CS Han, S Pitluck, ML Land, LJ Hauser, N Krypides, N Mikhailova, Z He, L Wu, JD Van Nostrand, B Henrissat, Q He, PA Lawson, RS Tanner, LR Lynd, J Wiegel, MW Fields, AP Arkin, CW Schadt, BS Stevenson, MJ McInerney, Y Yang, H Dong, RL Huhnke, JR Mielenz, S-Y Ding, ME Himmel, S Taghavi, D. van der Lelie, EM Rubin, and J-Z Zhou. (2010) Genome Announcement: Sequencing of Multiple Clostridia Genomes Related to Biomass Conversion and Biofuels Production. Journal of Bacteriology, 192:6494-6496
  5. Hollister EE, CW Schadt, R Ansley, AV Palumbo and TW Boutton. (2010) Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains. Soil Biology and Biochemistry. 10:1816-1824
  6. Miller LD, JJ Mosher, A Venkateswaran, ZK Yang, AV Palumbo, TJ Phelps, M Podar, CW Schadt and M Keller. (2010) Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments. BMC Microbiology 10:149
  7. Reganold, JP, PK Andrews, JR Reeve, L Carpenter-Boggs, CW Schadt, JR Alldredge, CF Ross, NM Davies, and J Zhou (2010) Fruit and soil quality of organic and conventional strawberry agroecosystems. PLoS ONE. 5:
  8. Reeve J, CW Schadt, L Carpenter-Boggs, S Kang, J Zhou and JP Reganold. (2010) Effects of soil type and farm management on soil ecological functional genes and microbial activities. ISME Journal 4:1099–1107
  9. Zhang F, W-M Wu, JC Parker, T Mehlhorn, SD Kelly, KM Kemner, G Zhang, CW Schadt, SC Brooks, CS Criddle, DB Watson and PM Jardine (2010) Kinetic analysis and modeling of oleate and ethanol stimulated uranium (VI) bio-reduction in contaminate sediments under sulfate reduction conditions. Journal of Hazardous Materials 183:482-489

2009

  1. Austin, EA, HF Castro, KT Sides, CW Schadt and AT Classen. (2009) Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation. Soil Biology and Biogeochemistry, 41:514-520.
  2. Berthrong, ST, CW Schadt, G Piñeiro and RB Jackson. (2009) Afforestation Alters the Composition of Functional Genes in Soil and Biogeochemical Processes in South American Grasslands. Applied and Environmental Microbiology, 75:6240-6248
  3. Madden AS, Palumbo AV, Ravel B, Vishnivetskaya TA, Phelps TJ, Schadt CW, and CC Brandt (2009) Donor-dependent extent of uranium reduction for bioremediation of contaminated sediment microcosms, Journal of Environmental Quality, 38:53-60.
  4. Waldron, PJ, L-Y Wu, JD Van Nostrand, CW Schadt, DB Watson, PM Jardine, AV Palumbo, TC Hazen, J-Z Zhou. (2009) Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environmental Science and Technology. 43:3529-3534.

2008

  1. Baker SE, Thykaer J, Adney WS, Brettin TS, Brockman FJ, D’haeseleer P, Diego A Martinez, Miller RM, Rokhsar DS, Schadt CW, Torok T, Tuskan G, Bennett J, Berka RM, Briggs SP, Heitman J, Taylor J, Turgeon BG, Werner-Washburne M and ME Himmel. (2008) Fungal Genome Sequencing and Bioenergy. Fungal Biology Reviews. 22:1-5.
  2. Nemergut DR, Townsend AR, Sattin SR, Freeman KR, Fierer N, Neff JC, Bowman WD, Schadt CW, Weintraub MN and SK Schmidt. (2008) The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: Implications for carbon and nitrogen cycling. Environmental Microbiology, 10:3093–3105.
  3. Porter TM*, Schadt CW*, Rizvi L, Martin AP; Schmidt SK; Scott-Denton L; Vilgalys R, and JM Moncalvo. (2008) Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Molecular Phylogenetics and Evolution. 46:635-644 (*Equal Contribution)
  4. Schmidt SK, Sobieniak–Wiseman LC, Kageyama SA, Halloy SRP and CW Schadt. (2008) Mycorrhizal and dark-septate fungi in plant roots above 4720 meters elevation in the Andes and Rocky Mountains. Arctic, Antarctic and Alpine Research. 40:576-583
  5. Zhou JZ, Kang S, Schadt CW, and CT Garten. (2008) Spatial Scaling of Functional Gene Diversity across Various Microbial Taxa. Proceedings of the National Academy of Sciences, 105:7768-7773.

2007

  1. He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Wu WM, Gu B, Jardine P, Criddle CS, and J-Z Zhou. (2007) GeoChip: A novel comprehensive microarray for investigating biogeochemical and environmental processes. ISME Journal 1:67-77 (>250 citations)
  2. Garten CT, Kang SH, Schadt CW, Brice DJ, and J-Z Zhou. (2007) Variability in Forest Soil Properties and Processes at Spatial Scales from One Meter to One Kilometer. Soil Biology and Biogeochemistry, 39:2621-2627
  3. Gao H, Yang ZK, Gentry TJ, Wu L, Schadt CW, and J-Z Zhou. (2007). Microarray-based Analysis of Microbial Community RNAs by Whole Community RNA Amplification (WCRA). Applied and Environmental Microbiology, 73:563-571.

2006

  1. Rodríguez-Martínez EM, Pérez EX, Schadt CW, Zhou J, and 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
  2. Gentry TJ, Wickham, GS, Schadt CW, He Z, and J Zhou. (2006) Microarray Applications in Microbial Ecology Research. Microbial Ecology, 52:159-175. (>100 citations)
  3. Hwang C, Wu WM, Gentry TJ, Carley J, Schadt CW, Carroll SL, Watson D, Jardine PM, Zhou J, Hickey RF, Criddle CS, and MW Fields. (2006) Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor, Applied Microbiology and Biotechnology, 71:748-760
  4. Wu L, Liu X, Schadt CW, and J Zhou. (2006) Microarray-based analysis of subpicogram quantities of microbial community DNA. Applied and Environmental Microbiology, 72:4931-4941.
  5. Liebich J., Schadt CW, Chong SC, Rhee SK, and J Zhou. (2006) Improvement of oligonucleotide probe design criteria for the development of functional gene microarrays for environmental applications. Applied and Environmental Microbiology, 72:1688-1691

2005 and Older

  1. Meyer AF, Lipson DA, Martin AP, Schadt CW, and SK Schmidt. (2004) Molecular and metabolic characterization of cold tolerant, alpine soil Psuedomonas sensu stricto. Applied and Environmental Microbiology. 70:483-489
  2. Schadt CW, Martin AP, Lipson DA and SK Schmidt. (2003). Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359-1361
  3. Lipson DA, Schadt CW and SK Schmidt. (2002) Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt. Microbial Ecology 43:307-314.
  4. Schadt CW, Mullen RB and SK Schmidt. (2001) Isolation and phylogenetic identification of a dark septate endophyte of the alpine plant Ranunculus adoneus. New Phytologist 150:747-754.
  5. Lipson DA, Schadt CW, Schmidt SK and RK Monson. (1999) Ectomycorrhizal transfer of amino acid-nitrogen to the alpine sedge Kobresia myosuroides. New Phytologist 142:163-167.

BOOK CHAPTERS

  1. Reganold JP, Andrews PK, Reeve JR, Carpenter-Boggs L, Schadt CW, Alldredge JR, Ross CF, Davies NM and JZ Zhou. (2013) Organic Versus Conventional Strawberry Agroecosystem. In: Sustainable Soil Management (D. Rooney, ed). CRC Press, Pg185-212
  2. Keller M, Schadt CW and AV Palumbo. (2008) Single Cell Genomics. In: Accessing Uncultivated Microorganisms (K. Zengler, ed) American Society for Microbiology Press, Washington DC.
  3. Schmidt SK, Wilson K, Meyer AF, Schadt CW, Porter TM and JM Moncalvo. (2008) The Missing Fungi – New Insights from Culture-Independent Molecular Studies of Soil. In: Accessing Uncultivated Microorganisms (K. Zengler, ed) American Society for Microbiology Press, Washington DC.
  4. Gentry TJ, Schadt CW, He Z, and J Zhou. (2007). Functional Gene Arrays for Microbial Community Analysis. In: Manual of Environmental Microbiology (Crawford et al., eds) American Society for Microbiology Press, Washington DC.
  5. Schadt CW and J Zhou. Advances in Microarrays for Soil Microbial Community Analyses. (2006) In Soil Biology Volume 8: Nucleic Acids and Proteins in Soil (Nannipieri, P. & Smalla K., eds). Springer-Verlag, Pp189-203.
  6. Schadt CW, Leibich J, Chong SC, Gentry TJ, He Z, Pan H, and J Zhou. (2005) Design and Use of Functional Gene Microarrays (FGAs) for the Characterization of Microbial Communities. In Methods in Microbiology Volume 33: Microbial Imaging (Savidge & Pothoulakis, eds). Academic Press, Pg331-368

OTHER PUBLICATIONS

  1. Schadt CW, Classen AT. (2007) Book Review: Soil Microbiology, Ecology and Biochemistry.: EA Paul (ed). Soil Science Society of America Journal, 71:1420
  2. Schadt, CW. (2014). New found ‘silence’ on a southern, suburban, summer night. Belle Rêve Literary Journal 14(3):54-56

PATENTS

  1. Pelletier DA, Weston DJ, Schadt CW, Doktycz MJ and GA Tuskan 2013. Plant Growth Promoting Rhizobacterium. Filed January 2013, No. 13/747,995, Patent Pending.

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