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Volumn 8, Issue 3, 2013, Pages

Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; IRON DERIVATIVE; NITROGENASE; RNA 16S; GROUND WATER; HUMIC SUBSTANCE; IRON; PHOSPHATE; URANIUM; VANADIUM;

EID: 84874637810     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057819     Document Type: Article
Times cited : (20)

References (38)
  • 1
    • 84874588257 scopus 로고    scopus 로고
    • Ecology, Microbial
    • Schaechter M. editor, Oxford: Elsevier
    • Konopka A Ecology, Microbial. In: Schaechter M, editor. Encyclopedia of Microbiology. Oxford: Elsevier. 91-106.
    • Encyclopedia of Microbiology , pp. 91-106
    • Konopka, A.1
  • 2
    • 69949110616 scopus 로고    scopus 로고
    • How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats
    • Lin B, Westerhoff HV, Röling WFM, (2009) How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats. Enviro Microbiol 11: 2425-2433.
    • (2009) Enviro Microbiol , vol.11 , pp. 2425-2433
    • Lin, B.1    Westerhoff, H.V.2    Röling, W.F.M.3
  • 3
    • 0037817377 scopus 로고    scopus 로고
    • Determination of In Situ Bacterial Growth Rates in Aquifers and Aquifer Sediments
    • Mailloux BJ, Fuller ME, (2003) Determination of In Situ Bacterial Growth Rates in Aquifers and Aquifer Sediments. Appl Environ Microbiol 69: 3798-3808.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 3798-3808
    • Mailloux, B.J.1    Fuller, M.E.2
  • 4
    • 58549102477 scopus 로고    scopus 로고
    • Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments
    • Holmes DE, O'Neil RA, Chavan MA, N'Guessan LA, Vrionis HA, et al. (2008) Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments. ISME J 3: 216-230.
    • (2008) ISME J , vol.3 , pp. 216-230
    • Holmes, D.E.1    O'Neil, R.A.2    Chavan, M.A.3    N'Guessan, L.A.4    Vrionis, H.A.5
  • 6
    • 10744231694 scopus 로고    scopus 로고
    • Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
    • Anderson RT, Vrionis HA, Ortiz-Bernad I, Resch CT, Long PE, et al. (2003) Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer. Appl Environ Microbiol 69: 5884-5891.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 5884-5891
    • Anderson, R.T.1    Vrionis, H.A.2    Ortiz-Bernad, I.3    Resch, C.T.4    Long, P.E.5
  • 7
    • 0024191542 scopus 로고
    • Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese
    • Lovley DR, Phillips ER, (1988) Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 54: 1472-1480.
    • (1988) Appl Environ Microbiol , vol.54 , pp. 1472-1480
    • Lovley, D.R.1    Phillips, E.R.2
  • 9
    • 2442638056 scopus 로고    scopus 로고
    • Vanadium Respiration by Geobacter metallireducens: Novel Strategy for In Situ Removal of Vanadium from Groundwater
    • Ortiz-Bernad I, Anderson RT, Vrionis HA, Lovley DR, (2004) Vanadium Respiration by Geobacter metallireducens: Novel Strategy for In Situ Removal of Vanadium from Groundwater. Appl Environ Microbiol 70: 3091-3095.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 3091-3095
    • Ortiz-Bernad, I.1    Anderson, R.T.2    Vrionis, H.A.3    Lovley, D.R.4
  • 10
    • 70449095186 scopus 로고    scopus 로고
    • Investigating different mechanisms for biogenic selenite transformations: Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica
    • Pearce CI, Pattrick RAD, Law N, Charnock JC, Coker VS, et al. (2009) Investigating different mechanisms for biogenic selenite transformations: Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica. Environ Technol 30: 1313-1326.
    • (2009) Environ Technol , vol.30 , pp. 1313-1326
    • Pearce, C.I.1    Pattrick, R.A.D.2    Law, N.3    Charnock, J.C.4    Coker, V.S.5
  • 11
    • 79956110173 scopus 로고    scopus 로고
    • Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater
    • Williams KH, Long PE, Davis JA, Wilkins MJ, N'Guessan AL, et al. (2011) Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater. Geomicro J 28: 519-539.
    • (2011) Geomicro J , vol.28 , pp. 519-539
    • Williams, K.H.1    Long, P.E.2    Davis, J.A.3    Wilkins, M.J.4    N'Guessan, A.L.5
  • 12
    • 84874617545 scopus 로고    scopus 로고
    • Integrative analysis of the interactions between Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation
    • Barlett M, Zhuang K, Mahadevan R, Lovley DR, (2011) Integrative analysis of the interactions between Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation. Biogeosciences Discuss 8: 11337-11357.
    • (2011) Biogeosciences Discuss , vol.8 , pp. 11337-11357
    • Barlett, M.1    Zhuang, K.2    Mahadevan, R.3    Lovley, D.R.4
  • 13
    • 67449110763 scopus 로고    scopus 로고
    • Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater
    • Mouser PJ, N'Guessan AL, Elifantz H, Holmes DE, Williams KH, et al. (2009) Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater. Environ Sci Technol 43: 4386-4392.
    • (2009) Environ Sci Technol , vol.43 , pp. 4386-4392
    • Mouser, P.J.1    N'Guessan, A.L.2    Elifantz, H.3    Holmes, D.E.4    Williams, K.H.5
  • 14
    • 76349121789 scopus 로고    scopus 로고
    • Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer
    • N'Guessan AL, Elifantz H, Nevin KP, Mouser PJ, Methe B, et al. (2010) Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer. ISME J 4: 253-266.
    • (2010) ISME J , vol.4 , pp. 253-266
    • N'Guessan, A.L.1    Elifantz, H.2    Nevin, K.P.3    Mouser, P.J.4    Methe, B.5
  • 15
    • 77955249738 scopus 로고    scopus 로고
    • Expression of acetate permease-like (apl) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations
    • Elifantz H, N'Guessan LA, Mouser PJ, Williams KH, Wilkins MJ, et al. (2010) Expression of acetate permease-like (apl) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations. FEMS Microbiol Ecol 73: 441-449.
    • (2010) FEMS Microbiol Ecol , vol.73 , pp. 441-449
    • Elifantz, H.1    N'Guessan, L.A.2    Mouser, P.J.3    Williams, K.H.4    Wilkins, M.J.5
  • 16
    • 36849085899 scopus 로고    scopus 로고
    • Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments
    • Holmes DE, O'Neil RA, Vrionis HA, N'Guessan LA, Ortiz-Bernad I, et al. (2007) Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments. ISME J 1: 663-677.
    • (2007) ISME J , vol.1 , pp. 663-677
    • Holmes, D.E.1    O'Neil, R.A.2    Vrionis, H.A.3    N'Guessan, L.A.4    Ortiz-Bernad, I.5
  • 17
    • 78349248545 scopus 로고    scopus 로고
    • Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)
    • Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, et al. (2010) Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microb Biotech 4: 55-63.
    • (2010) Microb Biotech , vol.4 , pp. 55-63
    • Wilkins, M.J.1    Callister, S.J.2    Miletto, M.3    Williams, K.H.4    Nicora, C.D.5
  • 19
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 20
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5
  • 21
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
    • Letunic I, Bork P, (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475-W478.
    • (2011) Nucleic Acids Res , vol.39
    • Letunic, I.1    Bork, P.2
  • 22
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wisniewski JR, Zougman A, Nagaraj N, Mann M, (2009) Universal sample preparation method for proteome analysis. Nat Meth 6: 359-362.
    • (2009) Nat Meth , vol.6 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 23
    • 33751248265 scopus 로고    scopus 로고
    • Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry
    • Kelly RT, Page JS, Luo Q, Moore RJ, Orton DJ, et al. (2006) Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry. Anal Chem 78: 7796-7801.
    • (2006) Anal Chem , vol.78 , pp. 7796-7801
    • Kelly, R.T.1    Page, J.S.2    Luo, Q.3    Moore, R.J.4    Orton, D.J.5
  • 24
    • 50149117169 scopus 로고    scopus 로고
    • Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
    • Kim S, Gupta N, Pevzner PA, (2008) Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases. J Prot Res 7: 3354-3363.
    • (2008) J Prot Res , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 28
    • 34548184733 scopus 로고    scopus 로고
    • Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis
    • Denef VJ, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF, (2007) Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis. J Prot Res 6: 3152-3161.
    • (2007) J Prot Res , vol.6 , pp. 3152-3161
    • Denef, V.J.1    Shah, M.B.2    VerBerkmoes, N.C.3    Hettich, R.L.4    Banfield, J.F.5
  • 29
    • 40149105737 scopus 로고    scopus 로고
    • Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens
    • Segura D, Mahadevan R, Juarez K, Lovley DR (2008) Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PloS Comput Biol 4.
    • (2008) PloS Comput Biol 4
    • Segura, D.1    Mahadevan, R.2    Juarez, K.3    Lovley, D.R.4
  • 30
    • 78650298909 scopus 로고    scopus 로고
    • In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling
    • Mahadevan R, Palsson Bò, Lovley DR, (2011) In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat Rev Micro 9: 39-50.
    • (2011) Nat Rev Micro , vol.9 , pp. 39-50
    • Mahadevan, R.1    Palsson, B.O.2    Lovley, D.R.3
  • 31
    • 54549114308 scopus 로고    scopus 로고
    • Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron donor
    • Ding YHR, Hixson KK, Aklujkar MA, Lipton MS, Smith RD, et al. (2008) Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron donor. Biochim Biophys Acta 1784: 1935-1941.
    • (2008) Biochim Biophys Acta , vol.1784 , pp. 1935-1941
    • Ding, Y.H.R.1    Hixson, K.K.2    Aklujkar, M.A.3    Lipton, M.S.4    Smith, R.D.5
  • 32
    • 34250829079 scopus 로고    scopus 로고
    • Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid
    • Tang YJJ, Chakraborty R, Martin HG, Chu J, Hazen TC, et al. (2007) Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 73: 3859-3864.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 3859-3864
    • Tang, Y.J.J.1    Chakraborty, R.2    Martin, H.G.3    Chu, J.4    Hazen, T.C.5
  • 33
    • 0036276689 scopus 로고    scopus 로고
    • Potential for bioremediation of uranium-contaminated aquifers with microbial U(VI) reduction
    • Finneran KT, Anderson RT, Nevin KP, Lovley DR, (2002) Potential for bioremediation of uranium-contaminated aquifers with microbial U(VI) reduction. Soil Sed Contam 11: 339-357.
    • (2002) Soil Sed Contam , vol.11 , pp. 339-357
    • Finneran, K.T.1    Anderson, R.T.2    Nevin, K.P.3    Lovley, D.R.4
  • 34
    • 17644385506 scopus 로고    scopus 로고
    • The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective
    • Coppi MV, (2005) The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiol 151: 1239-1254.
    • (2005) Microbiol , vol.151 , pp. 1239-1254
    • Coppi, M.V.1
  • 35
    • 84861217024 scopus 로고    scopus 로고
    • Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens
    • Tremblay P-L, Lovley DR, (2012) Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens. J Bact 194: 2248-2253.
    • (2012) J Bact , vol.194 , pp. 2248-2253
    • Tremblay, P.-L.1    Lovley, D.R.2
  • 36
    • 0034353620 scopus 로고    scopus 로고
    • N-2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species
    • Bazylinski DA, Dean AJ, Schuler D, Phillips EJP, Lovley DR, (2000) N-2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species. Environ Microbiol 2: 266-273.
    • (2000) Environ Microbiol , vol.2 , pp. 266-273
    • Bazylinski, D.A.1    Dean, A.J.2    Schuler, D.3    Phillips, E.J.P.4    Lovley, D.R.5
  • 37
    • 84862836623 scopus 로고    scopus 로고
    • Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer
    • Campbell KM, Kukkadapu RK, Qafoku NP, Peacock AD, Lesher E, et al. (2012) Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer. Appl Geochem 27: 1499-1511.
    • (2012) Appl Geochem , vol.27 , pp. 1499-1511
    • Campbell, K.M.1    Kukkadapu, R.K.2    Qafoku, N.P.3    Peacock, A.D.4    Lesher, E.5
  • 38
    • 84865482228 scopus 로고    scopus 로고
    • Timing the Onset of Sulfate Reduction over Multiple Subsurface Acetate Amendments by Measurement and Modeling of Sulfur Isotope Fractionation
    • Druhan JL, Steefel CI, Molins S, Williams KH, Conrad ME, et al. (2012) Timing the Onset of Sulfate Reduction over Multiple Subsurface Acetate Amendments by Measurement and Modeling of Sulfur Isotope Fractionation. Environ Sci Technol 46: 8895-8902.
    • (2012) Environ Sci Technol , vol.46 , pp. 8895-8902
    • Druhan, J.L.1    Steefel, C.I.2    Molins, S.3    Williams, K.H.4    Conrad, M.E.5


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