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Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing

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Abstract

Stable isotope probing (SIP) was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with 13C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24 h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosm with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant 13C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U(VI) reduction in the less reduced sample. 13C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron (III) reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U(VI)-reducing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobacter and Desulfosporosinus. The findings suggest that ethanol biostimulates the U(VI)-reducing microbial community by first serving as an electron donor for nitrate, sulfate, iron (III) and U(VI) reduction, and acetate which then functions as electron donor for U(VI) reduction and carbon source for microbial growth.

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References

  1. Lovley D R, Phillips E J. Reduction of uranium by Desulfovibrio desulfuricans. Applied and Environmental Microbiology, 1992, 58 (3): 850–856

    CAS  Google Scholar 

  2. Anderson R T, Vrionis H A, Ortiz-Bernad I, Resch C T, Long P E, Dayvault R, Karp K, Marutzky S, Metzler D R, Peacock A, White D C, Lowe M, Lovley D R. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Applied and Environmental Microbiology, 2003, 69(10): 5884–5891

    Article  CAS  Google Scholar 

  3. Istok J D, Senko J M, Krumholz L R, Watson D, Bogle M A, Peacock A, Chang Y J, White D C. In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer. Environmental Science & Technology, 2004, 38(2): 468–475

    Article  CAS  Google Scholar 

  4. Coates J D, Ellis D J, Gaw C V, Lovley D R. Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. International Journal of Systematic Bacteriology, 1999, 49(Pt 4): 1615–1622

    Article  CAS  Google Scholar 

  5. Wu W M, Carley J, Gentry T, Ginder-Vogel M A, Fienen M, Mehlhorn T, Yan H, Caroll S, Pace M N, Nyman J, Luo J, Gentile M E, Fields M W, Hickey R F, Gu B, Watson D, Cirpka O A, Zhou J, Fendorf S, Kitanidis P K, Jardine P M, Criddle C S. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of u(VI) and geochemical control of u(VI) bioavailability. Environmental Science & Technology, 2006, 40(12): 3986–3995

    Article  CAS  Google Scholar 

  6. Wu W M, Carley J, Fienen M, Mehlhorn T, Lowe K, Nyman J, Luo J, Gentile M E, Rajan R, Wagner D, Hickey R F, Gu B, Watson D, Cirpka O A, Kitanidis P K, Jardine P M, Criddle C S. Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 1. Conditioning of a treatment zone. Environmental Science & Technology, 2006, 40(12): 3978–3985

    Article  CAS  Google Scholar 

  7. Wu W M, Carley J, Luo J, Ginder-Vogel M A, Cardenas E, Leigh M B, Hwang C, Kelly S D, Ruan C, Wu L, Van Nostrand J, Gentry T, Lowe K, Mehlhorn T, Carroll S, Luo W, Fields MW, Gu B, Watson D, Kemner K M, Marsh T, Tiedje J, Zhou J, Fendorf S, Kitanidis P K, Jardine P M, Criddle C S. In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environmental Science & Technology, 2007, 41(16): 5716–5723

    Article  CAS  Google Scholar 

  8. Wu W M, Carley J, Green S J, Luo J, Kelly S D, Van Nostrand J, Lowe K, Mehlhorn T, Carroll S, Boonchayanant B, Löfller F E, Watson D, Kemner K M, Zhou J, Kitanidis P K, Kostka J E, Jardine P M, Criddle C S. Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface. Environmental Science & Technology, 2010, 44(13): 5104–5111

    Article  CAS  Google Scholar 

  9. Cardenas E, Wu WM, Leigh MB, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis PK, Jardine PM, Zhou J, Criddle CS, Marsh TL, Tiedje JM. Microbial communities in contaminated sediments associated with bioremediation of uranium to submicromolar levels. Applied Environmental Microbiology, 2008, 74(12): 3718–3729

    Article  CAS  Google Scholar 

  10. Hwang C, Wu W, Gentry T J, Carley J, Corbin G A, Carroll S L, Watson D B, Jardine P M, Zhou J, Criddle C S, Fields M W. Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME Journal, 2009, 3(1): 47–64

    Article  CAS  Google Scholar 

  11. Friedrich M W. Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Current Opinion in Biotechnology, 2006, 17(1): 59–66

    Article  CAS  Google Scholar 

  12. Whiteley A S, Manefield M, Lueders T. Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies. Current Opinion in Biotechnology, 2006, 17(1): 67–71

    Article  CAS  Google Scholar 

  13. Evershed R P, Crossman Z M, Bull I D, Mottram H, Dungait J A, Maxfield P J, Brennand E L. 13C-Labelling of lipids to investigate microbial communities in the environment. Current Opinion in Biotechnology, 2006, 17(1):72–82

    Article  CAS  Google Scholar 

  14. Uhlik O, Leewis M C, Strejcek M, Musilova L, Mackova M, Leigh M B, Macek T. Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnology Advances, 2013, 31(2): 154–165

    Article  CAS  Google Scholar 

  15. Luo J, Wu W, Fienen M N, Jardine P M, Mehlhorn T L, Watson D B, Cirpka O A, Criddle C S, Kitanidis P K. A nested-cell approach for in situ remediation. Ground Water, 2006, 44(2): 266–274

    Article  CAS  Google Scholar 

  16. Hwang C, Wu W M, Gentry T J, Carley J, Carroll S L, Schadt C, Watson D, Jardine P M, Zhou J, Hickey R F, Criddle C S, Fields M W. Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor. Applied Microbiology and Biotechnology, 2006, 71(5): 748–760

    Article  CAS  Google Scholar 

  17. Wu W M, Watson D B, Luo J, Carley J, Mehlhorn T, Kitanidis P K, Jardine P M, Criddle C S. Surge block method for controlling well clogging and sampling sediment during bioremediation. Water Research, 2013, 47(17): 6566–6573

    Article  CAS  Google Scholar 

  18. Leigh M B, Pellizari V H, Uhlík O, Sutka R, Rodrigues J, Ostrom N E, Zhou J, Tiedje J M. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME Journal, 2007, 1(2): 134–148

    Article  CAS  Google Scholar 

  19. Ashelford K E, Chuzhanova N A, Fry J C, Jones A J, Weightman A J. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Applied and Environmental Microbiology, 2006, 72(9): 5734–5741

    Article  CAS  Google Scholar 

  20. Ashelford K E, Chuzhanova N A, Fry J C, Jones A J, Weightman A J. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Applied and Environmental Microbiology, 2005, 71(12): 7724–7736

    Article  CAS  Google Scholar 

  21. Cole J R, Chai B, Farris R J, Wang Q, Kulam S A, McGarrell D M, Garrity GM, Tiedje JM. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Research, 2005, 33(Database issue): D294–D296

    CAS  Google Scholar 

  22. Lovley D R, Phillips E J, Gorby Y A, Landa E R. Microbial reduction of uranium. Nature, 1991, 350(6317): 413–416

    Article  CAS  Google Scholar 

  23. Wu Q, Sanford R A, Löffler F E. Uranium(VI) reduction by Anaeromyxobacter dehalogenans strain 2CP-C. Applied and Environmental Microbiology, 2006, 72(5): 3608–3614

    Article  CAS  Google Scholar 

  24. Zhou P, Gu B. Extraction of oxidized and reduced forms of uranium from contaminated soils: effects of carbonate concentration and pH. Environmental Science & Technology, 2005, 39(12): 4435–4440

    Article  CAS  Google Scholar 

  25. Lovley D R, Phillips E J P, Gorby Y A, Landa E R. Microbial reduction of uranium. Nature, 1991, 350(6317): 413–416

    Article  CAS  Google Scholar 

  26. Suzuki Y, Kelly SD, Kemner KM, Banfield JF: Enzymatic U(VI) reduction by Desulfosporosinus species. Radiochimica acta, 2004, 92(1): 11–16

    Article  CAS  Google Scholar 

  27. Nyman J L, Marsh T L, Ginder-Vogel M A, Gentile M, Fendorf S, Criddle C. Heterogeneous response to biostimulation for U(VI) reduction in replicated sediment microcosms. Biodegradation, 2006, 17(4): 303–316

    Article  CAS  Google Scholar 

  28. Cummings D E, Caccavo F Jr, Spring S, Rosenzweig R F. Ferribacterium limneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments. Archives of Microbiology, 1999, 171(3): 183–188

    Article  CAS  Google Scholar 

  29. Beller H R, Chain P S G, Letain T E, Chakicherla A, Larimer F W, Richardson P M, Coleman M A, Wood A P, Kelly D P. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. Journal of Bacteriology, 2006, 188(4): 1473–1488

    Article  CAS  Google Scholar 

  30. Wolfe A J. The acetate switch. Microbiology and Molecular Biology Reviews, 2005, 69(1): 12–50

    Article  CAS  Google Scholar 

  31. Senko J M, Istok J D, Suflita J M, Krumholz L R. In-situ evidence for uranium immobilization and remobilization. Environmental Science & Technology, 2002, 36(7): 1491–1496

    Article  CAS  Google Scholar 

  32. Wu W M, Gu B, Fields M W, Gentile M, Ku Y K, Tiquias S, Nyman J, Zhou J, Jardine P M, Criddle C S. Reduction uranium (VI) by denitrifying biomass. Bioremediation Journal, 2005, 9(1): 49–61

    Article  CAS  Google Scholar 

  33. Wu W M, Hickey R F, Zeikus J G. Characterization of metabolic performance of methanogenic granules treating brewery wastewater: role of sulfate-reducing bacteria. Applied and Environmental Microbiology, 1991, 57(12): 3438–3449

    CAS  Google Scholar 

  34. Mohanty S R, Kollah B, Hedrick D B, Peacock A D, Kukkadapu R K, Roden E E. Biogeochemical processes in ethanol stimulated uranium-contaminated subsurface sediments. Environmental Science & Technology, 2008, 42(12): 4384–4390

    Article  CAS  Google Scholar 

  35. Drake H L, Küsel K, Matthies C. Ecological consequences of the phylogenetic and physiological diversities of acetogens. Antonie van Leeuwenhoek, 2002, 81(1-4): 203–213

    Article  CAS  Google Scholar 

  36. Heo J, Wolfe M T, Staples C R, Ludden P W. Converting the NiFeS carbon monoxide dehydrogenase to a hydrogenase and a hydroxylamine reductase. Journal of Bacteriology, 2002, 184(21): 5894–5897

    Article  CAS  Google Scholar 

  37. Magli A, Rainey F A, Leisinger T. Acetogenesis from dichloromethane by a two-component mixed culture comprising a novel bacterium. Applied and Environmental Microbiology, 1995, 61(8): 2943–2949

    CAS  Google Scholar 

  38. O’Loughlin E J, Kelly S D, Cook R E, Csencsits R, Kemner K M. Reduction of uranium(VI) by mixed iron(II)/iron(III) hydroxide (green rust): formation of UO2 nanoparticles. Environmental Science & Technology, 2003, 37(4): 721–727

    Article  Google Scholar 

  39. Lovley D R, Coates J D, Blunt-Harris E L, Phillips E J P, Woodward J C. Humic substances as electron acceptors for microbial respiration. Nature, 1996, 382(6590): 445–448

    Article  CAS  Google Scholar 

  40. Finneran K T, Johnsen C V, Lovley D R. Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). International Journal of Systematic and Evolutionary Microbiology, 2003, 53(Pt 3): 669–673

    Article  CAS  Google Scholar 

  41. Lovley D R, Roden E E, Phillips E J P, Woodward J C. Enzymatic iron and uranium reduction by sulfate-reducing bacteria. Marine Geology, 1993, 113(1-2): 41–53

    Article  CAS  Google Scholar 

  42. Lovley D R, Phillips E J P, Gorby Y A, Landa E R. Microbial reduction of uranium. Nature, 1991, 350(6317): 413–416

    Article  CAS  Google Scholar 

  43. Basso O, Caumette P, Magot M. Desulfovibrio putealis sp. nov., a novel sulfate-reducing bacterium isolated from a deep subsurface aquifer. International Journal of Systematic and Evolutionary Microbiology, 2005, 55(Pt 1): 101–104

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA

    Mary Beth Leigh, Erick Cardenas, Terence L. Marsh & James M. Tiedje

  2. Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA

    Mary Beth Leigh

  3. Department of Civil and Environmental Engineering, Center for Sustainable Development & Global Competitiveness, Codiga Resource Recovery Center, Stanford University, Stanford, CA, 94305-4020, USA

    Wei-Min Wu & Craig S. Criddle

  4. Department of Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technicka 3, 166 28, Prague, Czech Republic

    Ondrej Uhlik

  5. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Sue Carroll, Terry Gentry, Jizhong Zhou & Philip Jardine

  6. Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA

    Jizhong Zhou

  7. Department of Crop and Soil Sciences, Texas A&M University, College Station, TX, 77843, USA

    Terry Gentry

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  1. Mary Beth Leigh
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  2. Wei-Min Wu
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Correspondence to Mary Beth Leigh or Wei-Min Wu.

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Leigh, M.B., Wu, WM., Cardenas, E. et al. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing. Front. Environ. Sci. Eng. 9, 453–464 (2015). https://doi.org/10.1007/s11783-014-0721-6

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  • DOI: https://doi.org/10.1007/s11783-014-0721-6

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