James M. Tiedje, Primary Publications (2014-present):

  1. Cole, J.R.., Q. Wang, J.A. Fish, B. Chai, D.M. McGarrell, Y. Sun, C.T. Brown, A. Porras- Alfaro, C.R. Kuske and J.M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucl Acids Res. 42, Database issue:D633-D642; doi: 10.1093/nar/gkt1244 [PubMed]

  2. Deng, J., I. Brettar, C. Luo, J. Auchtung, K.T. Konstantinidis, J.L. Rodrigues, M. Höfle and J.M. Tiedje. 2014. Stability, genotypic and phenotypic diversity of the Shewanella baltica population in the redox transition zone of the Baltic Sea. Environ Microbiol. 16(6):1854-1866; doi: 10.1111/1462-2920.12344 [PubMed]

  3. Yang, Y., J. Quensen, J. Mathieu, Q. Wang, J. Wang, M. Li, J.M. Tiedje and P.J. Alvarez. 2014. Pyrosequencing reveals higher impact of silver nanoparticles than Ag+ on the microbial community structure of activated sludge. Water Res. 48:317-325; doi: 10.1016/j.watres.2013.09.046 [PubMed]

  4. Zhang, Y., S.A. Boyd, B.J. Teppen, J.M. Tiedje and H. Li. 2014. Organic acids enhance bioavailability of tetracycline in water to Escherichia coli for uptake and expression of antibiotic resistance. Water Res. 65:98-106; doi: 10.1016/j.watres.2014.07.021 [PubMed]

  5. Penton, C.R., V.V. Gupta, J.M. Tiedje, S.M. Neate, K. Ophel-Keller, M. Gillings, P. Harvey, A. Pham and D.K. Roget. 2014. Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing. PLoS ONE 09(4):e93893; doi: 10.1371/journal.pone.0093893 [PubMed]

  6. Smalla, K. and J.M. Tiedje. 2014. Editorial overview: Ecology and industrial microbiology. Curr Opin Microbiol. 19:v-vii; doi: 10.1016/j.mib.2014.06.011 [PubMed]

  7. Siles, J.A., C.T. Rachid, I. Sampedro, I. García-Romera and J.M. Tiedje. 2014. Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment. PLoS One 9(7):e103035; doi: 10.1371/journal.pone.0103035 [PubMed]

  8. Luo, C., R.L.M. Rodriguez., E. Johnston, L. Wu, L. Cheng, K. Xue, Q. Tu, Y. Deng, Z. He, Z. Shi, M. Yuan, S. Rebecca, D. Li, Y. Luo, E.A.G. Schuur, P. Chain, J. Tiedje, J. Zhou and K. Konstantinidis. 2014. Soil microbial community responses to a decade of warming as revealed by comparative Metagenomics. Appl Environ Microbiol. 80:1777-1786. doi: 10.1128/AEM.03712-13 [PubMed]

  9. Vital, M., C.R. Penton, Q. Wang, V.B. Young, D.A. Antonopoulo, M.L. Sogin, H.G. Morrison, L. Raffals, E.B. Chang, G.B. Huffnagle, T.M. Schmidt, J.R. Cole and J.M. Tiedje. 2014. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome. 2013 Mar 4;1(1):8; doi: 10.1186/2049-2618-1-8 [PubMed]

  10. Young, V.B., L.H. Raffals, S.M. Huse, M. Vital, D. Dai, P.D. Schloss, J.M. Brulc, D.A. Antonopoulos, R.L. Arrieta, J.H. Kwon, K.G. Reddy, N.A. Hubert, S.L. Grim, J.H. Vineis, S. Dalal, H.G. Morrison, A.M. Eren, F. Meyer, T.M. Schmidt, J.M. Tiedje, E.B. Chang and M.L. Sogin. 2014. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 1(1):9; doi: 10.1186/2049-2618-1-9 [PubMed]

  11. 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. PNAS 111(9):E836-E845; doi: 10.1073/pnas.1324044111 [PubMed]

  12. Penton, C.R., J.L. Deenik, B.N. Popp, G.L. Bruland, P. Engstrom, J. Mueller, A. Worden and J.M. Tiedje. 2014. Assessing nitrogen transformations in a flooded agroecosystem using the isotope pairing technique and nitrogen functional gene abundances. Soil Sci. 179(1):2-10; doi: 10.1097/SS.0000000000000038

  13. Zhang, Y., S.A. Boyd, B.J. Teppen, J. M Tiedje and H. Li. 2014. Role of Tetracycline Speciation in the Bioavailability to a Bioreporter for Uptake and Expression of Antibiotic Resistance. Environ. Sci. Technol. 48(9):4893-4900; doi: 10.1021/es5003428 [PubMed]

  14. Howe, A.C., J.K. Jansson, S.A. Malfatti, S.G. Tringe, J.M. Tiedje and C.T. Brown. 2014. Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A. 111(13):4904-4909; doi: 10.1073/pnas.1402564111 [PubMed]

  15. Vital, M., A.C. Howe and J.M. Tiedje. 2014. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio. 5(2):e00889. doi: 10.1128/mBio.00889-14 [PubMed] PMC3994512

  16. Kyrpides, N.C., P. Hugenholtz, J.A. Eisen, T. Woyke, M. Göker, C.T. Parker, R. Amann, B.J. Beck, P.S.G. Chain, J. Chun, R.R. Colwell, A. Danchin, P. Dawyndt, T. Dedeurwaerdere, E.F. DeLong, J.C. Detter, P. De Vos, T. J. Donohue, X-Z. Dong, D.S. Ehrlich, C. Fraser, R. Gibbs, J. Gilbert, P. Gilna, F.O. Glöckner, J.K. Jansson, J.D. Keasling, R. Knight, D. Labeda, A. Lapidus, J-S. Lee, W-J. Li, J. MA, V. Markowitz, E.R.B. Moore, M. Morrison, F. Meyer, K.E. Nelson, M. Ohkuma, C.A. Ouzounis, N. Pace, J. Parkhill, N. Qin, R. Rossello-Mora, J. Sikorski, D. Smith, M. Sogin, R. Stevens, U. Stingl, K. Suzuki, D. Taylor, J.M. Tiedje, B. Tindall, M. Wagner, G. Weinstock, J. Weissenbach, O. White, J. Wang, L. Zhang, Y-G. Zhou, D. Field, W.B. Whitman, G.M. Garrity, H-P. Klenk. 2014. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biol. 12(8): e1001920; doi: 10.1371/journal.pbio.1001920 [PubMed]

  17. Paula F.S., J.L.M. Rodrigues, J. Zhou, L. Wu, R.C. Mueller, B.S. Mirza, B.J.M. Bohannan, K. Nuesslein, 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(12):2988-2999; doi: 10.1111/mec.12786 [PubMed]

  18. Cole, J.R. and J.M. Tiedje. 2014. History and impact of RDP: A legacy from Carl Woese to microbiology. RNA Biol. 11(3):239-243; doi: 10.4161/rna.28306 [PubMed]

  19. Siles, J.A., C.T.C.C. Rachid, I. Sampedro, I. García-Romera and J.M Tiedje. 2014. Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment. PLoS ONE 9(7):e103035; doi: 10.1371/journal.pone.0103035 [PubMed]

  20. Liang, J., D. Li, Z. Shi, J.M. Tiedje, J. Zhou, E.A.G. Schuur, K.T. Konstantinidis and Y.i Luo. 2014. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation. Soil Biol Biochem. 80:127-135; doi: 10.1016/j.soilbio.2014.10.005

  21. Zaborin, A., D. Smith, K. Garfield, J. Quensen, B. Shakhsheer, M. Kade, M. Tirrell, J. Tiedje, J.A. Gilbert, O. Zaborina and J.C. Alverdy. 2014. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. MBio 5(5):e01361-14; doi: 10.1128/mBio.01361-14 [PubMed]

  22. Vital, M., B. Chai, B. Ostman, J. Cole, K.T. Konstantinidis and J.M. Tiedje. 2014. Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. ISME J. 9:1130-1140; doi: 10.1038/ismej.2014.204 [PubMed]

  23. Vital, M., J. Gao, M. Rizzo, T. Harrison and J.M. Tiedje. 2014. Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. ISME J. 9:832-833; doi: 10.1038/ismej.2014.179 [PubMed]

  24. Zhang, Y., S.A. Boyd, B.J. Teppen, J.M. Tiedje and H. Li. 2014. Organic acids enhance bioavailability of tetracycline in water to Escherichia coli for uptake and expression of antibiotic resistance. Water Res. 65:98-106; doi: 10.1016/j.watres.2014.07.021 [PubMed]

  25. Su, J.Q., L.J. Ding, K. Xue, H.Y. Yao, J. Quensen, S.J. Bai, W.X. Wei, J.S. Wu, J. Zhou, J.M. Tiedje and Y.G. Zhu. 2015. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol. 24(1):136-150; doi: 10.1111/mec.13010 [PubMed]

  26. Deng, J., Y. Gu, J. Zhang, K. Xue, Y. Qin, M. Yuan, H. Yin, Z. He, L. Wu, E.A. Schuur, J.M. Tiedje and J. Zhou. 2015. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Mol Ecol. 24(1):222-234; doi: 10.1111/mec.13015 [PubMed]

  27. Gillings, M.R., W.H. Gaze, A. Pruden, K. Smalla, J.M. Tiedje and Y-G. Zhu. 2014. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9(6):1269–1279; doi: 10.1038/ismej.2014.226 [PubMed]

  28. Vital, M., J.R. Harkema, M. Rizzo, J. Tiedje and C. Brandenberger. 2015. Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. J Immunology Res 2015, Article ID 892568:1-8; doi: 10.1155/2015/892568 [PubMed]

  29. He, R., M.J. Wooller, J.W. Pohlman, J.M. Tiedje and M.B. Leigh. 2015. Methane-derived carbon flow through microbial communities in arctic lake sediments. 2015. Environ Microbio. 17(9):3233-3250; doi: 10.1111/1462-2920.12773 [PubMed]

  30. Rachid, C., F.C. Balieiro, E.S. Fonseca, R.S. Peixoto, G.M. Chaer, J.M. Tiedje and A.S. Rosado. 2015. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations. PLoS ONE 10(2):e011851; doi: 10.1371/journal.pone.0118515 [PubMed]

  31. Zhang, P., W-M. Wu, J.D. Van Nostrand, Y. Deng, Z. He, T. Gihring, G. Zhang, C.W. Schadt, D. Watson, P. Jardine, C.S. Criddle, S. Brooks, T.L. Marsh, J.M. Tiedje, A.P. 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. Appl Environ Microbiol. 81(12):4164-4172; doi: 10.1128/AEM.00043-15 [PubMed]

  32. Li, B., Y. Yang, L. Ma, F. Ju, F. Guo, J.M. Tiedje and T. Zhang. 2015. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J Advance 9(11):2490-2502; doi: 10.1038/ismej.2015.59 [PubMed]

  33. Zhang, B., C.R. Penton, C. Xue, Q. Wang, T. Zheng and J.M. Tiedje. 2015. Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH. Appl Environ Microbiol. 81(13):4536-4545; doi: 10.1128/AEM.00111-15 [PubMed]

  34. Leigh, M.B., W-M. Wu, E. Cardenas, O. Uhlik, S. Carroll, T. Gentry, T.L. Marsh, J. Zhou, P. Jardine, C.S. Criddle and J.M. Tiedje. 2015. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing. Front of Environ Sci Engin 9(3):453-464; doi: 10.1007/s11783-014-0721-6

  35. Penton, C.R., D. St. Louis, A. Pham, J.R. Cole, L. Wu, Y. Luo, E.A.G. Schuur, J. Zhou, and J.M. Tiedje. 2015. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Front Microbiology 21 July 2015; doi: 10.3389/fmicb.2015.00746 [PubMed]

  36. Singh, P., T.K. Teal, T.L. Marsh, J.M. Tiedje, R. Mosci, K. Jernigan, A. Zell, D.W. Newton, H. Salimnia, P. Lephart, D. Sundin, W. Khalife, R.A. Britton, J.T. Rudrik and S.D. Manning. 2015. Intestinal microbial communities associated with acute enteric infections and disease recovery. Microbiome 3:45; doi: 10.1186/s40168-015-0109-2 [PubMed]

  37. Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M Tiedje and J. R Cole. 2015. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome 3:32; doi: 10.1186/s40168-015-0093-6 [PubMed]

  38. Stedtfeld, R.D., Y.C. Liu, T.M. Stedtfeld, T. Kostic, M. Kronlein, O. Srivannavit, W.T. Khalife, J.M. Tiedje, E. Gulari, M. Hughes, B. Etchebarne and S.A. Hashsham. 2015. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomed Microdevices 17(5):9994; doi: 10.1007/s10544-015-9994-1 [PubMed]

  39. Hemme, C.L., Q. Tu, Z. Shi, Y. Qin, W. Gao, Y. Deng, J.D. Van Nostrand, L. Wu, Z. He, P.S.G. Chain, S.G. Tringe, M.W. Fields, E.M. Rubin, J.M. Tiedje, T.C. Hazen, A.P. Arkin and J. Zhou. 2015. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front. Microbiol. 6:1205; doi: 10.3389/fmicb.2015.01205 [PubMed]

  40. Navarrete, A.A., A.M. Venturini, K.M. Meyer, A.M. Klein, J.M. Tiedje, B.J.M. Bohannan, K. Nüsslein, S.M. Tsai and J.L.M. Rodrigues. 2015. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Front. Microbiol. 6:1443; doi: 10.3389/fmicb.2015.01443 [PubMed]

  41. Seyrig, G., R.D. Stedtfelda, D.M. Tourloussea, F. Ahmada, K. Towerya, A.M. Cupples, J.M. Tiedje and Syed A. Hashsham. 2015. Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J Microbiological Methods 119:223–227; doi: 10.1016/j.mimet.2015.11.004 [PubMed]

  42. Jesus, E. da C., C. Liang, J.F. Quensen, E. Susilawati, R.D. Jackson, T.C. Balser and J.M. Tiedje. 2015. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States. ePub ahead of print 26 Dec 2015. GCB Bioenergy 8(2): 481-494; doi: 10.1111/gcbb.12289

  43. Xue, C.. C.R. Penton, B. Zhang, M. Zhao, D.E. Rothstein, D.J. Mladenoff, J.A. Forrester, Q. Shen and J.M. Tiedje. 2016. Soil fungal and bacterial responses to conversion of open land to short rotation woody biomass crops. GCB Bioenergy 8(4):723–736; doi: 10.1111/gcbb.12303

  44. Ma, L., Y. Xia, B. Li, Y. Yang, L-G. Li, J.M. Tiedje and T. Zhang. 2016. Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces. Environ. Sci. Technol. 50(1):420–427; doi: 10.1021/acs.est.5b03522 [PubMed]

  45. Guo, J., J.R. Cole, Q. Zhang, C.T. Brown and J.M. Tiedje. 2016. Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Appl Environ Microbiol. 82(1):157-166; doi: 10.1128/AEM.02772-15 [PubMed]

  46. Liang, C., E.daC. Jesus, D.S. Duncan, J.F. Quensen, R.D. Jackson, T.C. Balser and J.M. Tiedje. 2016. Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA. Soil Biology and Biochem 94:173-180; doi: 10.1016/j.soilbio.2015.11.020 [PubMed]

  47. Karkman, A., T. Johnson, C. Lyra, R. Stedtfeld, M. Tamminen, J.M. Tiedje and M. Virta. 2016. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol Ecol.  Jan 31 pii: fiw014. First published online; doi: 10.1093/femsec/fiw014 [PubMed].

  48. Stedtfeld, R., M. Williams, U. Fakhera, T. Johnson, T. Stedtfeld, F. Wang, W. Khalife, M. Hughes, B. Etchebarne, J.M. Tiedje, and S. Hashsham. 2016. Antimicrobial resistance (AR) dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol Ecol. Feb 4 pii: fiw020First published online; doi: 10.1093/femsec/fiw020 [PubMed]

  49. Penton, C.R., V.V. Gupta, J. Yu, J.M. Tiedje. 2016. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons. Front Microbiol. 7:824.; doi: 10.3389/fmicb.2016.00824 [PubMed]

  50. Johnson, T.A., R.D. Stedtfeld, Q. Wang, J.R. Cole, S.A. Hashsham, T. Looft, Y-G. Zhu, and J.M. Tiedje. 2016. Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture. mBio 7(2):e02214-15; doi: 10.1128/mBio.02214-15 [PubMed]

  51. de Carvalho, T. S., E. d. C. Jesus. ,J. Barlow, T.A. Gardner, I.C. Soares, J.M. Tiedje, and F. M. d. S.Moreira. 2016. Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria. Ecology 97(10):2760–2771; doi: 10.1002/ecy.1513

  52. Xue, K., M.M. Yuan, J. Xie, D. Li, Y. Qin, L.E. Hale, L. Wu, Y. Deng, Z. He, J.D. Van Nostrand, Y. Luo, J.M. Tiedje, and J. Zhou. 2016. Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming. mBio 7(5): e00976-16; doi: 10.1128/mBio.00976-16 [PubMed]

  53. Hambright, W.S., J. Deng, J.M. Tiedje, I. Brettar, and J.L.M. Rodrigues. 2016. Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions. mSphere 1(5), pii: e00158-16; doi: 10.1128/mSphere.00158-16 [PubMed]

  54. SmallaK., P. SimonetJ. Tiedjeand E. Topp. 2016. Emergence of Antibiotic Resistant Pathogens and One Health--Editorial and Opinion: Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance. FEMS Microbiol Ecol: first published online Sept 2016; doi: 10.1093/femsec/fiw172

  55. Wang, F., R.D. Stedtfeld, O-S. Kim, B. Chai, L. Yang, T.M. Stedtfeld, S.G. Hong, D. Kim, H.S. Lim, S.A. Hashsham, J.M. Tiedje, and W.J. Sul. 2016. Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils. Environ Sci Technol. (ePub before print, October 2016); doi: 10.1021/acs.est.6b02863

  56. Hamaoui, Jr., G.S., J.L.M. Rodrigues, B.J.M. Bohannan, J.M. Tiedje, and K. Nüsslein. 2016. Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondônia, Brazil. Appl Soil Ecol 107: 48-56; doi: 10.1016/j.apsoil.2016.05.012

  57. Garoutte, A., E. Cardenas, J. Tiedje, and A. Howe. 2016. Methodologies for probing the metatranscriptome of grassland soil. J Microbiol Methods 131: 122–129; doi: 10.1016/j.mimet.2016.10.018 [PubMed]

  58. 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. Tiedje, and J. Zhou. 2016. NifH-Harboring Bacterial Community Composition Across an Alaskan Permafrost Thaw Gradient. Front Microbiol 7:1894 (e42149); doi: 10.3389/fmicb.2016.01894 [PubMed]

  59. Choi, J., F. Yang, R. Stepanauskas, E. Cardenas, A. Garoutte, R. Williams, J. Flater, J.M. Tiedje, K.S. Hofmockel, B. Gelder, and A. Howe. 2016. Strategies to improve reference databases for soil microbiomes. ISME J, December 9 Epub ahead of print; doi: 10.1038/ismej.2016.168 [PubMed]