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Volumn 13, Issue 18-19, 2013, Pages 2910-2920

Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP)

Author keywords

Aerobic PAH degradation; BACTRAP; Functional metaproteomics; Groundwater natural attenuation; Microbiology; Protein SIP

Indexed keywords

CARBON; FLUORENE; GROUND WATER; NAPHTHALENE; POLYCYCLIC AROMATIC HYDROCARBON;

EID: 84885043115     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200569     Document Type: Article
Times cited : (70)

References (45)
  • 1
    • 77149152780 scopus 로고    scopus 로고
    • Environmental proteomics: analysis of structure and function of microbial communities
    • Schneider, T., Riedel, K., Environmental proteomics: analysis of structure and function of microbial communities. Proteomics 2010, 10, 785-798.
    • (2010) Proteomics , vol.10 , pp. 785-798
    • Schneider, T.1    Riedel, K.2
  • 2
    • 84864035417 scopus 로고    scopus 로고
    • Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
    • Hettich, R. L., Sharma, R., Chourey, K., Giannone, R. J., Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr. Opin. Microbiol. 2012, 15, 373-380.
    • (2012) Curr. Opin. Microbiol. , vol.15 , pp. 373-380
    • Hettich, R.L.1    Sharma, R.2    Chourey, K.3    Giannone, R.J.4
  • 3
    • 79551500036 scopus 로고    scopus 로고
    • Less label, more free: approaches in label-free quantitative mass spectrometry
    • Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
    • (2011) Proteomics , vol.11 , pp. 535-553
    • Neilson, K.A.1    Ali, N.A.2    Muralidharan, S.3    Mirzaei, M.4
  • 5
    • 0032032875 scopus 로고    scopus 로고
    • Tracing the assimilation of organic compounds using delta C-13 analysis of unique amino acids in the bacterial peptidoglycan cell wall
    • Pelz, O., Cifuentes, L. A., Hammer, B. T., Kelley, C. A. et al., Tracing the assimilation of organic compounds using delta C-13 analysis of unique amino acids in the bacterial peptidoglycan cell wall. FEMS Microbiol. Ecol. 1998, 25, 229-240.
    • (1998) FEMS Microbiol. Ecol. , vol.25 , pp. 229-240
    • Pelz, O.1    Cifuentes, L.A.2    Hammer, B.T.3    Kelley, C.A.4
  • 6
    • 0032560228 scopus 로고    scopus 로고
    • Direct linking of microbial populations to specific biogeochemical processes by C-13-labelling of biomarkers
    • Boschker, H. T. S., Nold, S. C., Wellsbury, P., Bos, D. et al., Direct linking of microbial populations to specific biogeochemical processes by C-13-labelling of biomarkers. Nature 1998, 392, 801-805.
    • (1998) Nature , vol.392 , pp. 801-805
    • Boschker, H.T.S.1    Nold, S.C.2    Wellsbury, P.3    Bos, D.4
  • 7
    • 34248137874 scopus 로고    scopus 로고
    • Methodological considerations for the use of stable isotope probing in microbial ecology
    • Neufeld, J. D., Dumont, M. G., Vohra, J., Murrell, J. C., Methodological considerations for the use of stable isotope probing in microbial ecology. Microbial. Ecol. 2007, 53, 435-442.
    • (2007) Microbial. Ecol. , vol.53 , pp. 435-442
    • Neufeld, J.D.1    Dumont, M.G.2    Vohra, J.3    Murrell, J.C.4
  • 8
    • 77649104651 scopus 로고    scopus 로고
    • Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing
    • Herrmann, S., Kleinsteuber, S., Chatzinotas, A., Kuppardt, S. et al., Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ. Microbiol. 2010, 12, 401-411.
    • (2010) Environ. Microbiol. , vol.12 , pp. 401-411
    • Herrmann, S.1    Kleinsteuber, S.2    Chatzinotas, A.3    Kuppardt, S.4
  • 10
    • 84867574489 scopus 로고    scopus 로고
    • Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
    • Seifert, J., Taubert, M., Jehmlich, N., Schmidt, F. et al., Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom. Rev. 2012, 31, 683-697.
    • (2012) Mass Spectrom. Rev. , vol.31 , pp. 683-697
    • Seifert, J.1    Taubert, M.2    Jehmlich, N.3    Schmidt, F.4
  • 11
    • 55549089274 scopus 로고    scopus 로고
    • Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures
    • Jehmlich, N., Schmidt, F., von Bergen, M., Richnow, H. H. et al., Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2008, 2, 1122-1133.
    • (2008) ISME J. , vol.2 , pp. 1122-1133
    • Jehmlich, N.1    Schmidt, F.2    von Bergen, M.3    Richnow, H.H.4
  • 12
    • 53049085850 scopus 로고    scopus 로고
    • Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP)
    • Jehmlich, N., Schmidt, F., Hartwich, M., von Bergen, M. et al., Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP). Rapid Commun. Mass Spectrom. 2008, 22, 2889-2897.
    • (2008) Rapid Commun. Mass Spectrom. , vol.22 , pp. 2889-2897
    • Jehmlich, N.1    Schmidt, F.2    Hartwich, M.3    von Bergen, M.4
  • 13
    • 84860854996 scopus 로고    scopus 로고
    • Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium
    • Morris, B. E. L., Herbst, F. A., Bastida, F., Seifert, J. et al., Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium. Environ. Microbiol. Rep. 2012, 4, 297-306.
    • (2012) Environ. Microbiol. Rep. , vol.4 , pp. 297-306
    • Morris, B.E.L.1    Herbst, F.A.2    Bastida, F.3    Seifert, J.4
  • 14
    • 84871289127 scopus 로고    scopus 로고
    • Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium
    • Taubert, M., Vogt, C., Wubet, T., Kleinsteuber, S. et al., Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J. 2012, 6, 2291-2301.
    • (2012) ISME J. , vol.6 , pp. 2291-2301
    • Taubert, M.1    Vogt, C.2    Wubet, T.3    Kleinsteuber, S.4
  • 15
    • 0036023980 scopus 로고    scopus 로고
    • Natural attenuation: what does the subsurface have in store?
    • Roling, W. F., van Verseveld, H. W., Natural attenuation: what does the subsurface have in store? Biodegradation 2002, 13, 53-64.
    • (2002) Biodegradation , vol.13 , pp. 53-64
    • Roling, W.F.1    van Verseveld, H.W.2
  • 16
    • 0028166469 scopus 로고
    • Comparison between geochemical and biological estimates of subsurface microbial activities
    • Phelps, T. J., Murphy, E. M., Pfiffner, S. M., White, D. C., Comparison between geochemical and biological estimates of subsurface microbial activities. Microbial. Ecol. 1994, 28, 335-349.
    • (1994) Microbial. Ecol. , vol.28 , pp. 335-349
    • Phelps, T.J.1    Murphy, E.M.2    Pfiffner, S.M.3    White, D.C.4
  • 18
    • 53749102061 scopus 로고    scopus 로고
    • Microbial biodegradation of polyaromatic hydrocarbons
    • Peng, R. H., Xiong, A. S., Xue, Y., Fu, X. Y. et al., Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol. Rev. 2008, 32, 927-955.
    • (2008) FEMS Microbiol. Rev. , vol.32 , pp. 927-955
    • Peng, R.H.1    Xiong, A.S.2    Xue, Y.3    Fu, X.Y.4
  • 19
    • 31244434671 scopus 로고    scopus 로고
    • Toxicity testing of 16 priority polycyclic aromatic hydrocarbons using Lumistox
    • Loibner, A. P., Szolar, O. H., Braun, R., Hirmann, D., Toxicity testing of 16 priority polycyclic aromatic hydrocarbons using Lumistox. Environ. Toxicol. Chem. 2004, 23, 557-564.
    • (2004) Environ. Toxicol. Chem. , vol.23 , pp. 557-564
    • Loibner, A.P.1    Szolar, O.H.2    Braun, R.3    Hirmann, D.4
  • 21
    • 79952575710 scopus 로고    scopus 로고
    • Bacteria-mediated PAH degradation in soil and sediment
    • Lu, X. Y., Zhang, T., Fang, H. H., Bacteria-mediated PAH degradation in soil and sediment. Appl. Microbiol. Biotechnol. 2011, 89, 1357-1371.
    • (2011) Appl. Microbiol. Biotechnol. , vol.89 , pp. 1357-1371
    • Lu, X.Y.1    Zhang, T.2    Fang, H.H.3
  • 22
    • 79957985337 scopus 로고    scopus 로고
    • Anaerobic degradation of non-substituted aromatic hydrocarbons
    • Meckenstock, R. U., Mouttaki, H., Anaerobic degradation of non-substituted aromatic hydrocarbons. Curr. Opin. Biotechnol. 2011, 22, 406-414.
    • (2011) Curr. Opin. Biotechnol. , vol.22 , pp. 406-414
    • Meckenstock, R.U.1    Mouttaki, H.2
  • 23
    • 53749102061 scopus 로고    scopus 로고
    • Microbial biodegradation of polyaromatic hydrocarbons
    • Peng, R. H., Xiong, A. S., Xue, Y., Fu, X. Y. et al., Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol. Rev. 2008, 32, 927-955.
    • (2008) FEMS Microbiol. Rev. , vol.32 , pp. 927-955
    • Peng, R.H.1    Xiong, A.S.2    Xue, Y.3    Fu, X.Y.4
  • 25
    • 22044437693 scopus 로고    scopus 로고
    • In situ assessment of biodegradation potential using biotraps amended with 13C-labeled benzene or toluene
    • Geyer, R., Peacock, A. D., Miltner, A., Richnow, H. H. et al., In situ assessment of biodegradation potential using biotraps amended with 13C-labeled benzene or toluene. Environ. Sci. Technol. 2005, 39, 4983-4989.
    • (2005) Environ. Sci. Technol. , vol.39 , pp. 4983-4989
    • Geyer, R.1    Peacock, A.D.2    Miltner, A.3    Richnow, H.H.4
  • 26
    • 34249809594 scopus 로고    scopus 로고
    • Benzene oxidation under sulfate-reducing conditions in columns simulating in situ conditions
    • Vogt, C., Gödeke, S., Treutler, H. C., Weiss, H. et al., Benzene oxidation under sulfate-reducing conditions in columns simulating in situ conditions. Biodegradation 2007, 18, 625-636.
    • (2007) Biodegradation , vol.18 , pp. 625-636
    • Vogt, C.1    Gödeke, S.2    Treutler, H.C.3    Weiss, H.4
  • 27
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 28
    • 24144480557 scopus 로고    scopus 로고
    • DBToolkit: processing protein databases for peptide-centric proteomics
    • Martens, L., Vandekerckhove, J., Gevaert, K., DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics 2005, 21, 3584-3585.
    • (2005) Bioinformatics , vol.21 , pp. 3584-3585
    • Martens, L.1    Vandekerckhove, J.2    Gevaert, K.3
  • 29
    • 70349912263 scopus 로고    scopus 로고
    • False discovery rates of protein identifications: a strike against the two-peptide rule
    • Gupta, N., Pevzner, P. A., False discovery rates of protein identifications: a strike against the two-peptide rule. J. Proteome Res. 2009, 8, 4173-4181.
    • (2009) J. Proteome Res. , vol.8 , pp. 4173-4181
    • Gupta, N.1    Pevzner, P.A.2
  • 30
    • 80155195169 scopus 로고    scopus 로고
    • Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP)
    • Taubert, M., Baumann, S., von Bergen, M., Seifert, J., Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP). Anal. Bioanal. Chem. 2011, 401, 1975-1982.
    • (2011) Anal. Bioanal. Chem. , vol.401 , pp. 1975-1982
    • Taubert, M.1    Baumann, S.2    von Bergen, M.3    Seifert, J.4
  • 31
    • 29144431588 scopus 로고    scopus 로고
    • Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics
    • Snijders, A. P., de Koning, B., Wright, P. C., Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics. J. Proteome Res. 2005, 4, 2185-2191.
    • (2005) J. Proteome Res. , vol.4 , pp. 2185-2191
    • Snijders, A.P.1    de Koning, B.2    Wright, P.C.3
  • 32
    • 58149354855 scopus 로고    scopus 로고
    • Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization
    • Huang, W. E., Ferguson, A., Singer, A. C., Lawson, K. et al., Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization. Appl. Environ. Microbiol. 2009, 75, 234-241.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 234-241
    • Huang, W.E.1    Ferguson, A.2    Singer, A.C.3    Lawson, K.4
  • 33
    • 31144439476 scopus 로고    scopus 로고
    • Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans
    • Hirano, S., Haruki, M., Takano, K., Imanaka, T. et al., Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans. Appl. Microbiol. Biotechnol. 2006, 69, 672-681.
    • (2006) Appl. Microbiol. Biotechnol. , vol.69 , pp. 672-681
    • Hirano, S.1    Haruki, M.2    Takano, K.3    Imanaka, T.4
  • 34
    • 4544255889 scopus 로고    scopus 로고
    • Isolation and characterization of Xanthobacter polyaromaticivorans sp. nov. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions
    • Hirano, S., Kitauchi, F., Haruki, M., Imanaka, T. et al., Isolation and characterization of Xanthobacter polyaromaticivorans sp. nov. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions. Biosci. Biotech. Bioch. 2004, 68, 557-564.
    • (2004) Biosci. Biotech. Bioch. , vol.68 , pp. 557-564
    • Hirano, S.1    Kitauchi, F.2    Haruki, M.3    Imanaka, T.4
  • 35
    • 33144455400 scopus 로고    scopus 로고
    • The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: evolutionary implications for two gene clusters and novel regulatory control
    • Jeon, C. O., Park, M., Ro, H. S., Park, W. et al., The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: evolutionary implications for two gene clusters and novel regulatory control. Appl. Environ. Microbiol. 2006, 72, 1086-1095.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 1086-1095
    • Jeon, C.O.1    Park, M.2    Ro, H.S.3    Park, W.4
  • 36
    • 0035167509 scopus 로고    scopus 로고
    • Nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism
    • Zhou, N. Y., Fuenmayor, S. L., Williams, P. A., Nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol. 2001, 183, 700-708.
    • (2001) J. Bacteriol. , vol.183 , pp. 700-708
    • Zhou, N.Y.1    Fuenmayor, S.L.2    Williams, P.A.3
  • 37
    • 0034081192 scopus 로고    scopus 로고
    • Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated under various environmental conditions
    • Krooneman, J., Sliekers, A. O., Pedro Gomes, T. M., Forney, L. J. et al., Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated under various environmental conditions. FEMS Microbiol. Ecol. 2000, 32, 53-59.
    • (2000) FEMS Microbiol. Ecol. , vol.32 , pp. 53-59
    • Krooneman, J.1    Sliekers, A.O.2    Pedro Gomes, T.M.3    Forney, L.J.4
  • 38
    • 0025528777 scopus 로고
    • Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane monooxygenase activity
    • Brusseau, G. A., Tsien, H. C., Hanson, R. S., Wackett, L. P., Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane monooxygenase activity. Biodegradation 1990, 1, 19-29.
    • (1990) Biodegradation , vol.1 , pp. 19-29
    • Brusseau, G.A.1    Tsien, H.C.2    Hanson, R.S.3    Wackett, L.P.4
  • 39
    • 0034877347 scopus 로고    scopus 로고
    • Characterization of Rhodococcus opacus R7, a strain able to degrade naphthalene and o-xylene isolated from a polycyclic aromatic hydrocarbon-contaminated soil
    • Di Gennaro, P., Rescalli, E., Galli, E., Sello, G. et al., Characterization of Rhodococcus opacus R7, a strain able to degrade naphthalene and o-xylene isolated from a polycyclic aromatic hydrocarbon-contaminated soil. Res. Microbiol. 2001, 152, 641-651.
    • (2001) Res. Microbiol. , vol.152 , pp. 641-651
    • Di Gennaro, P.1    Rescalli, E.2    Galli, E.3    Sello, G.4
  • 40
    • 45549096541 scopus 로고    scopus 로고
    • Effectiveness of bacterial inoculum and mangrove plants on remediation of sediment contaminated with polycyclic aromatic hydrocarbons
    • Tam, N. F., Wong, Y. S., Effectiveness of bacterial inoculum and mangrove plants on remediation of sediment contaminated with polycyclic aromatic hydrocarbons. Mar. Pollut. Bull. 2008, 57, 716-726.
    • (2008) Mar. Pollut. Bull. , vol.57 , pp. 716-726
    • Tam, N.F.1    Wong, Y.S.2
  • 41
    • 35448975374 scopus 로고    scopus 로고
    • Naphthalene metabolism and growth inhibition by naphthalene in Polaromonas naphthalenivorans strain CJ2
    • Pumphrey, G. M., Madsen, E. L., Naphthalene metabolism and growth inhibition by naphthalene in Polaromonas naphthalenivorans strain CJ2. Microbiology 2007, 153, 3730-3738.
    • (2007) Microbiology , vol.153 , pp. 3730-3738
    • Pumphrey, G.M.1    Madsen, E.L.2
  • 42
    • 58849106145 scopus 로고    scopus 로고
    • Three types of antibiotics produced from Rhodococcus erythropolis strains
    • Kitagawa, W., Tamura, T., Three types of antibiotics produced from Rhodococcus erythropolis strains. Microbes Environ. 2008, 23, 167-171.
    • (2008) Microbes Environ. , vol.23 , pp. 167-171
    • Kitagawa, W.1    Tamura, T.2
  • 43
    • 4344610106 scopus 로고    scopus 로고
    • Characterization of the upper pathway genes for fluorene metabolism in Terrabacter sp. strain DBF63
    • Habe, H., Chung, J. S., Kato, H., Ayabe, Y. et al., Characterization of the upper pathway genes for fluorene metabolism in Terrabacter sp. strain DBF63. J. Bacteriol. 2004, 186, 5938-5944.
    • (2004) J. Bacteriol. , vol.186 , pp. 5938-5944
    • Habe, H.1    Chung, J.S.2    Kato, H.3    Ayabe, Y.4
  • 44
    • 84877750576 scopus 로고    scopus 로고
    • Cloning of dfdA genes from Terrabacter sp. strain DBF63 encoding dibenzofuran 4,4a-dioxygenase and heterologous expression in Streptomyces lividans
    • Kasuga, K., Nitta, A., Kobayashi, M., Habe, H. et al., Cloning of dfdA genes from Terrabacter sp. strain DBF63 encoding dibenzofuran 4, 4a-dioxygenase and heterologous expression in Streptomyces lividans. Appl. Microbiol. Biotechnol. 2013, 97, 4485-4498.
    • (2013) Appl. Microbiol. Biotechnol. , vol.97 , pp. 4485-4498
    • Kasuga, K.1    Nitta, A.2    Kobayashi, M.3    Habe, H.4
  • 45
    • 0028233145 scopus 로고
    • Evidence for a novel pathway in the degradation of fluorene by Pseudomonas sp. strain F274
    • Grifoll, M., Selifonov, S. A., Chapman, P. J., Evidence for a novel pathway in the degradation of fluorene by Pseudomonas sp. strain F274. Appl. Environ. Microbiol. 1994, 60, 2438-2449.
    • (1994) Appl. Environ. Microbiol. , vol.60 , pp. 2438-2449
    • Grifoll, M.1    Selifonov, S.A.2    Chapman, P.J.3


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