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2019 Publications

  1. Akondi RN, Sharma S, Trexler RV, Mouser PJ, Pfiffner SM. 2019. Microbial lipid biomarkers detected in deep subsurface black shales. Environmental Science-Processes & Impacts 21:291-307.
  2. Booker A, Hoyt D, Meulia T, Eder E, Nicora C, Purvine S, Daly R, Moore J, Wunch K, Pfiffner S, Lipton M, Mouser PJ, Wrighton KC, Wilkins MJ. 2019. Deep subsurface pressure stimulates metabolic plasticity in shale-colonizing Halanaerobium spp. Applied and Environmental Microbiology 85:e00018-19.
  3. Braun de Torrez EC, Brown VA, McCracken GF, Kunz TH. 2019. Sympatric bat species prey opportunistically on a major moth pest of pecans. Sustainability 11:6365.
  4. Catarino AI, Frutos A, Henry TB. 2019. Use of fluorescent-labelled nanoplastics (NPs) to demonstrate NP absorption is inconclusive without adequate controls. Science of the Total Environment 670:915-920.
  5. Chen HH, Yang ZK, Yip D, Morris RH, Lebreux SJ, Cregger MA, Klingeman DM, Hui DF, Hettich RL, Wilhelm SW, Wang GS, Loffler FE, Schadt CW. 2019. One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation. PLoS ONE 14.
  6. Conway M, Brumbaugh A, Xu T, Young A, Close D, Ripp S. Overview of in vivo imaging methods and instrumentation. In Barroso MM, Intes X (ed.), Imaging from cells to animals in vivo. Taylor & Francis Books, Inc., in press.
  7. Davern S, O’Neil D, Hallikainen H, O’Neil K, Allman S, Millet L, Retterer S, Doktycz M, Standaert R, Boll R, Van Cleve S, DePaoli D, Mirzadeh S. 2019. Microfluidics-based separation of actinium-225 from radium-225 for medical applications. Separation Science and Technology 54:1994-2002.
  8. Din G, Hasan F, Conway M, Denney B, Ripp S, Shah AA. 2019. Engineering a bioluminescent bioreporter from an environmentally-sourced mercury-resistant Enterobacter cloacae strain for the detection of bioavailable mercury. Journal of Applied Microbiology 127:1125-1134.
  9. Din G, Hasan F, Ripp S, Shah AA. 2019. Characterization of organic acid producing Aspergillus tubingensis FMS1 and its role in metals leaching from soil Geomicrobiology Journal 10.1080/01490451.2019.1701585.
  10. Im J, Mack EE, Seger ES, Loffler FE. 2019. Biotic and abiotic dehalogenation of 1,1,2-trichloro-1,2,2-trifluoroethane (CFC-113): Implications for bacterial detoxification of chlorinated ethenes. Environmental Science & Technology 53:11941-11948.
  11. Kaya D, Kjellerup BV, Chourey K, Hettich RL, Taggart DM, Löffler FE. 2019. Impact of fixed nitrogen availability on Dehalococcoides mccartyi reductive dechlorination activity. Environmental Science & Technology 10.1021/acs.est.9b04463.
  12. Kirkpatrick A, Xu T, Ripp S, Sayler G, Close D. 2019. Biotechnological advances in luciferase enzymes. In Suzuki H (ed.), Bioluminescence-Analytical Applications and Basic Biology 10.5772/intechopen.85313. IntechOpen, London, UK.
  13. Kleindienst S, Chourey K, Chen G, Murdoch RW, Higgins SA, Iyer R, Campagna SR, Mack EE, Seger ES, Hettich RL, Löffler FE. 2019. Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism. Applied and Environmental Microbiology 85:e02768-18.
  14. Kraev G, Rivkina E, Vishnivetskaya T, Belonosov A, van Huissteden J, Kholodov A, Smirnov A, Kudryavtsev A, Teshebaeva K, Zamolodchikov D. 2019. Methane in gas shows from boreholes in epigenetic permafrost of Siberian Arctic. Geosciences 9.
  15. Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Loffler FE, O’Malley MA, Martin HG, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD. 2019. Common principles and best practices for engineering microbiomes. Nature Reviews Microbiology 17:725-741.
  16. Liang R, Lau M, Vishnivetskaya T, Lloyd KG, Wang W, Wiggins J, Miller J, Pfiffner S, Rivkina EM, Onstott T. 2019. Predominance of anaerobic, spore-forming bacteria in metabolically active microbial communities from ancient Siberian permafrost. Applied and Environmental Microbiology 10.1128/aem.00560-19:AEM.00560-19.
  17. Liang X, Radosevich M, Löffler F, Schaeffer SM, Zhuang J. 2019. Impact of microbial iron oxide reduction on the transport of diffusible tracers and non-diffusible nanoparticles in soils. Chemosphere 220:391-402.
  18. Liang XL, Zhuang J, Loffler FE, Zhang YY, DeBruyn JM, Wilhelm SW, Schaeffer SM, Radosevich M. 2019. Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation. Environmental Microbiology 21:2043-2055.
  19. Manoharan L, Kozlowski JA, Murdoch RW, Löffler FE, Sousa FL, Schleper C. 2019. Metagenomes from coastal marine sediments give insights into the ecological role and cellular features of Loki– and Thorarchaeota. mBio 10:e02039-19.
  20. Moon J-W, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, Podar M, Ge X, Walian PJ, Smith HJ, Wu X, Zane GM, Walker KF, Thorgersen MP, Poole FL, Lui LM, Adams BG, De León KB, Brewer SS, Williams DE, Lowe KA, Rodriguez M, Mehlhorn TL, Pfiffner SM, Chakraborty R, Arkin AP, Wall JD, Fields MW, Adams MWW, Stahl DA, Elias DA, Hazen TC. 2019. Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. bioRxiv 10.1101/712562:712562.
  21. Olivatto GP, Martins MCT, Montagner CC, Henry TB, Carreira RS. 2019. Microplastic contamination in surface waters in Guanabara Bay, Rio de Janeiro, Brazil. Marine Pollution Bulletin 139:157-162.
  22. Orellana LH, Hatt JK, Iyer R, Chourey K, Hettich RL, Spain JC, Yang WH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT. 2019. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. Scientific Reports 9:17630.
  23. Patabadige DEW, Millet LJ, Aufrecht JA, Shankles PG, Standaert RF, Retterer ST, Doktycz MJ. 2019. Label-free time- and space-resolved exometabolite sampling of growing plant roots through nanoporous interfaces. Scientific Reports 9.
  24. Patsiou D, Kalman J, Fernandes TF, Henry TB. 2019. Differences in engineered nanoparticle surface physicochemistry revealed by investigation of changes in copper bioavailability during sorption to nanoparticles in the aqueous phase. Environmental Toxicology and Chemistry 38:925-935.
  25. Rodriguez-Perez A, James M, Donnan DW, Henry TB, Moller LF, Sanderson WG. 2019. Conservation and restoration of a keystone species: Understanding the settlement preferences of the European oyster (Ostrea edulis). Marine Pollution Bulletin 138:312-321.
  26. Rusley C, Onstott TC, Vishnivetskaya TA, Layton A, Chauhan A, Pfiffner SM, Whyte LG, Lau MCY. 2019. Metagenome-assembled genome of USC alpha AHI, a potential high-affinity methanotroph from Axel Heiberg Island, Canadian High Arctic. Microbiology Resource Announcements 8.
  27. Solis MIV, Abraham PE, Chourey K, Swift CM, Loffler FE, Hettich RL. 2019. Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater. Scientific Reports 9.
  28. Spirina EV, Kuleshov KV, Yunusova AK, Vishnivetskaya TA, Rivkina EM. 2019. Draft genome sequence of Microbacterium sp. Gd 4-13, isolated from Gydanskiy Peninsula permafrost sediments of marine origin. Microbiology Resource Announcements 8.
  29. Vannuci-Silva M, Cadore S, Henry TB, Umbuzeiro G. 2019. Higher silver bioavailability after nanoparticle dietary exposure in marine amphipods. Environmental Toxicology and Chemistry 38:806-810.
  30. Vishnivetskaya T, Spirina E, Shmakova L, Tutukina M, Li Z, Wu XF, Rivkina E. 2019. Metagenomes from late pleistocene ice complex sediments of the Siberian Arctic. Microbiology Resource Announcements 8.
  31. 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, Acevedo D, Agullo-Barcelo M, Alvarez PJJ, Alvarez-Cohen L, Andersen GL, de Araujo JC, Boehnke K, Bond P, Bott CB, Bovio P, Brewster RK, Bux F, Cabezas A, Cabrol L, Chen S, Criddle CS, Deng Y, Etchebehere C, Ford A, Frigon D, Gómez JS, Griffin JS, Gu AZ, Habagil M, Hale L, Hardeman SD, Harmon M, Horn H, Hu Z, Jauffur S, Johnson DR, Keller J, Keucken A, Kumari S, Leal CD, Lebrun LA, Lee J, Lee M, Lee ZMP, Li Y, Li Z, Li M, Li X, Ling F, Liu Y, Luthy RG, Mendonça-Hagler LC, de Menezes FGR, Meyers AJ, Mohebbi A, Nielsen PH, Ning D, Oehmen A, Palmer A, Parameswaran P, Park J, Patsch D, Reginatto V, de los Reyes FL, Rittmann BE, Robles AN, Rossetti S, Shan X, Sidhu J, Sloan WT, Smith K, de Sousa OV, Stahl DA, Stephens K, Tian R, Tiedje JM, Tooker NB, Tu Q, Van Nostrand JD, De los Cobos Vasconcelos D, Vierheilig J, Wagner M, Wakelin S, Wang A, Wang B, Weaver JE, Wells GF, West S, Wilmes P, Woo S-G, Wu L, Wu J-H, Wu L, Xi C, Xiao N, Xu M, Yan T, Yang Y, Yang M, Young M, Yue H, Zhang B, Zhang P, Zhang Q, Zhang Y, Zhang T, Zhang Q, Zhang W, Zhang Y, Zhou H, Zhou J, Wen X, Curtis TP, He Q, He Z, Brown M, 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, Global Water Microbiome Consortium. 2019. Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology 10.1038/s41564-019-0426-5.
  32. Xu T, Close D, Din G, Sayler G, Ripp S. 2019. Engineering autobioluminescent eukaryotic cells as tools for environmental and biomedical surveillance. In Belkin S, Freemont P (ed.), Handbook of Cell Biosensors. Springer Publishing, New York, NY.
  33. Xu T, Kirkpatrick A, Toperzer J, Ripp S, Close D. 2019. Improving estrogenic compound screening efficiency by using self-modulating, continuously bioluminescent human cell bioreporters expressing a synthetic luciferase. Toxicological Sciences 168:551-560.
  34. Yan J, Yang Y, Li XY, Loffler FE. 2019. Complete genome sequence of Dehalococcoides mccartyi strain FL2, a trichloroethene-respiring anaerobe isolated from pristine freshwater sediment. Microbiology Resource Announcements 8.
  35. Yanac K, Murdoch RW. 2019. Biotransformation of the fluorinated nonsteroidal anti-inflammatory pharmaceutical flurbiprofen in activated sludge results in accumulation of a recalcitrant fluorinated aromatic metabolite. Global Challenges 3. 10.1002/gch2.201800093.
  36. Yang L, Chen X, Zeng XF, Radosevich M, Ripp S, Zhuang J, Sayler G. Surface-adsorbed contaminants mediate the importance of chemotaxis and haptotaxis for bacterial transport through soils. Frontiers in Microbiology, in press.
  37. Yin Y, Yan J, Chen G, Murdoch FK, Pfisterer N, Löffler FE. 2019. Nitrous oxide is a potent inhibitor of bacterial reductive dechlorination. Environmental Science & Technology 53:692-701.