Utilization of a Detergent-Based Method for Direct Microbial Cellular Lysis/Proteome Extraction from Soil Samples for Metaproteomics Studies
Soil metaproteomics is a rapidly developing and rather complex field aimed at understanding the functionalities of soil microbial communities. One of the main challenges of such an approach is the availability of a robust and efficient protocol to extract proteins from soil microbes inhabiting this complex matrix. The wide range of soil types and the innumerable variations in soil properties confound this experimental goal. Here we present a detergent based, heat-assisted cellular lysis method coupled with trichloroacetic acid (TCA) precipitation of soil microbial proteins that has been developed in our lab and found to be reasonably robust and unbiased in extracting microbial proteins from a broad range of soils for downstream mass spectrometric characterizations of microbial metabolic activities in natural ecosystems.
Key wordsSoil proteomics Metaproteomics Protein extraction Biological mass spectrometry Soil protein extraction Cell lysis
Karuna Chourey and Robert L. Hettich acknowledge funding support from US Department of Energy, Genome Sciences Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US Department of Energy.
- 4.Elsas JD, Jansson JK, Trevors JT (2006) Modern soil microbiology books in soils, plants, and the environment, 2nd edn. CRC Press, Taylor and Francis Group, Boca RatonGoogle Scholar
- 5.Nannipieri P (ed) (2006) Role of stabilised enzymes in microbial ecology and enzyme extraction from soil with potential applications in soil proteomics, vol 8. Nucleic acids and proteins in soil. Springer-Verlag, Berlin, HeidelbergGoogle Scholar
- 6.Solaiman Z, Kashem MA, Matsumoto I (2007) Environmental proteomics: extraction and identification of protein in soil, vol 2. Soil biology, advanced techniques in soil microbiology. Springer-Verlag, Berlin, HeidelbergGoogle Scholar
- 8.Becher D, Bernhardt J, Fuchs S, Riedel K (2013) Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics 13(18–19):2895–2909Google Scholar
- 9.Ogunseitan OA (ed) (2006) Soil proteomics: extraction and analysis of proteins from soils, vol 8. Nucleic acid and proteins in soil. Berlin Heidelberg: Springer-Verlag.Google Scholar
- 17.Lau MC, Stackhouse BT, Layton AC, Chauhan A, Vishnivetskaya TA, Chourey K, Ronholm J, Mykytczuk NC, Bennett PC, Lamarche-Gagnon G, Burton N, Pollard WH, Omelon CR, Medvigy DM, Hettich RL, Pfiffner SM, Whyte LG, Onstott TC (2015) An active atmospheric methane sink in high Arctic mineral cryosols. ISME J 9(8):1880–1891CrossRefGoogle Scholar
- 18.Glass JB, Yu H, Steele JA, Dawson KS, Sun S, Chourey K, Pan C, Hettich RL, Orphan VJ (2014) Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments. Environ Microbiol 16(6):1592–1611CrossRefGoogle Scholar
- 19.Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich RL, Banfield JF (2013) Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J 7(4):800–816CrossRefGoogle Scholar
- 21.Nissen S, Liu X, Chourey K, Hettich RL, Wagner DD, Pfiffner SM, Loffler FE (2012) Comparative c-type cytochrome expression analysis in Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C grown with soluble and insoluble oxidized metal electron acceptors. Biochem Soc Trans 40(6):1204–1210CrossRefGoogle Scholar
- 23.Chourey K, Nissen S, Vishnivetskaya T, Shah M, Pfiffner S, Hettich RL, Loffler FE (2013) Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site. Proteomics 13(18–19):2921–2930Google Scholar