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Protein-Based Stable Isotope Probing (Protein-SIP): Applications for Studying Aromatic Hydrocarbon Degradation in Microbial Communities

Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

Protein-based stable isotope probing (protein-SIP) was developed to link microbial-specific metabolic function to phylogenetic information. The principle of the SIP-concept is the supplement of stable isotope-labelled compounds resulting in the labelling of microorganisms that are capable of utilizing these substrates as carbon source. The sum of all proteins reflects the functional status of the living organisms, so that the degree of heavy isotope incorporation represents a proxy for substrate assimilation and their activity. The main focus of this chapter is on the application of protein-SIP to elucidate metabolic processes in general and in particular those involved in the anaerobic degradation of aromatic hydrocarbons. Thus, the application of protein-SIP is a useful method to investigate the composition and the functional state of microbial communities.

References

  1. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Gruning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D (2018) The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46(W1):W537–W544CrossRefGoogle Scholar
  2. Angel R, Conrad R (2013) Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event. Environ Microbiol 15(10):2799–2815Google Scholar
  3. Bastida F, Jehmlich N, Lima K, Morris BE, Richnow HH, Hernandez T, von Bergen M, Garcia C (2015) The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment. J Proteome 135:162–169CrossRefGoogle Scholar
  4. Blazewicz SJ, Schwartz E (2011) Dynamics of (1)(8)O incorporation from H(2) (1)(8)O into soil microbial DNA. Microb Ecol 61(4):911–916CrossRefGoogle Scholar
  5. Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 4(4):484–494CrossRefGoogle Scholar
  6. Chen X, Wei S, Ji Y, Guo X, Yang F (2015) Quantitative proteomics using SILAC: principles, applications, and developments. Proteomics 15(18):3175–3192CrossRefGoogle Scholar
  7. Englander SW, Kallenbach NR (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 16(4):521–655CrossRefGoogle Scholar
  8. Fischer K, Majewsky M (2014) Cometabolic degradation of organic wastewater micropollutants by activated sludge and sludge-inherent microorganisms. Appl Microbiol Biotechnol 98(15):6583–6597CrossRefGoogle Scholar
  9. Grob C, Taubert M, Howat AM, Burns OJ, Dixon JL, Richnow HH, Jehmlich N, von Bergen M, Chen Y, Murrell JC (2015) Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environ Microbiol 17(10):4007–4018CrossRefGoogle Scholar
  10. Herbst FA, Bahr A, Duarte M, Pieper DH, Richnow HH, von Bergen M, Seifert J, Bombach P (2013) Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP). Proteomics 13(18–19):2910–2920Google Scholar
  11. Herbst FA, Lunsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH (2015) Enhancing metaproteomics – the value of models and defined environmental microbial systems. Proteomics 16(5):783–798CrossRefGoogle Scholar
  12. Jehmlich N, Schmidt F, Hartwich M, von Bergen M, Richnow HH, Vogt C (2008a) Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (protein-SIP). Rapid Commun Mass Spectrom 22(18):2889–2897CrossRefGoogle Scholar
  13. Jehmlich N, Schmidt F, von Bergen M, Richnow HH, Vogt C (2008b) Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures. ISME J 2(11):1122–1133CrossRefGoogle Scholar
  14. Jehmlich N, Vogt C, Lunsmann V, Richnow HH, von Bergen M (2016) Protein-SIP in environmental studies. Curr Opin Biotechnol 41:26–33CrossRefGoogle Scholar
  15. Justice NB, Li Z, Wang Y, Spaudling SE, Mosier AC, Hettich RL, Pan C, Banfield JF (2014) (15)N- and (2)H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity. Environ Microbiol 16(10):3224–3237CrossRefGoogle Scholar
  16. Kappelmeyer U, Wießner A, Kuschk P, Kästner M (2002) Operation of a universal test unit for planted soil filters – planted fixed bed reactor. Eng Life Sci 2(10):311–315CrossRefGoogle Scholar
  17. Kjeldal H, Zhou NA, Wissenbach DK, von Bergen M, Gough HL, Nielsen JL (2016) Genomic, proteomic, and metabolite characterization of gemfibrozil-degrading organism Bacillus sp. GeD10. Environ Sci Technol 50(2):744–755CrossRefGoogle Scholar
  18. Lagos L, Maruyama F, Nannipieri P, Mora M, Ogram A, Jorquera M (2015) Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini–review. J Soil Sci Plant Nutr 15(2):504–523Google Scholar
  19. Lünsmann V, Kappelmeyer U, Benndorf R, Martinez-Lavanchy PM, Taubert A, Adrian L, Duarte M, Pieper DH, von Bergen M, Muller JA, Heipieper HJ, Jehmlich N (2015) In-situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model. Environ Microbiol 18(4):1176–1186CrossRefGoogle Scholar
  20. Lünsmann V, Kappelmeyer U, Taubert A, Nijenhuis I, von Bergen M, Heipieper HJ, Muller JA, Jehmlich N (2016) Aerobic toluene degraders in the rhizosphere of a constructed wetland model show diurnal polyhydroxyalkanoate metabolism. Appl Environ Microbiol 82(14):4126–4132CrossRefGoogle Scholar
  21. Luo Y, Guo W, Ngo HH, Nghiem LD, Hai FI, Zhang J, Liang S, Wang XC (2014) A review on the occurrence of micropollutants in the aquatic environment and their fate and removal during wastewater treatment. Sci Total Environ 473-474:619–641CrossRefGoogle Scholar
  22. Pan C, Fischer CR, Hyatt D, Bowen BP, Hettich RL, Banfield JF (2011) Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics 10(4):M110 006049CrossRefGoogle Scholar
  23. Rettedal EA, Brozel VS (2015) Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218 O. Microbiology 4(2):208–219Google Scholar
  24. Sachsenberg T, Herbst FA, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O (2015) MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. J Proteome Res 14(2):619–627CrossRefGoogle Scholar
  25. Schroder P, Navarro-Avino J, Azaizeh H, Goldhirsh AG, DiGregorio S, Komives T, Langergraber G, Lenz A, Maestri E, Memon AR, Ranalli A, Sebastiani L, Smrcek S, Vanek T, Vuilleumier S, Wissing F (2007) Using phytoremediation technologies to upgrade waste water treatment in Europe. Environ Sci Pollut Res Int 14(7):490–497CrossRefGoogle Scholar
  26. Schwartz E (2007) Characterization of growing microorganisms in soil by stable isotope probing with (H2O)-O-18. Appl Environ Microbiol 73(8):2541–2546CrossRefGoogle Scholar
  27. Schwartz E (2009) Analyzing microorganisms in environmental samples using stable isotope probing with H2(18)O. Cold Spring Harb Protoc 2009(12):pdbprot5341CrossRefGoogle Scholar
  28. Taubert M, Jehmlich N, Vogt C, Richnow HH, Schmidt F, von Bergen M, Seifert J (2011) Time resolved protein-based stable isotope probing (protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments. Proteomics 11(11):2265–2274CrossRefGoogle Scholar
  29. Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, Buscot F, Richnow HH, von Bergen M, Seifert J (2012) Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J 6(12):2291–2301CrossRefGoogle Scholar
  30. Taubert M, Stockel S, Geesink P, Girnus S, Jehmlich N, von Bergen M, Rosch P, Popp J, Kusel K (2018) Tracking active groundwater microbes with D2 O labelling to understand their ecosystem function. Environ Microbiol 20(1):369–384CrossRefGoogle Scholar
  31. von Bergen M, Jehmlich N, Taubert M, Vogt C, Bastida F, Herbst FA, Schmidt F, Richnow HH, Seifert J (2013) Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J 7(10):1877–1885CrossRefGoogle Scholar
  32. Zhang R, Sioma CS, Thompson RA, Xiong L, Regnier FE (2002) Controlling deuterium isotope effects in comparative proteomics. Anal Chem 74(15):3662–3669CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany

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