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A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation

Environmental Science and Pollution Research volume 25, pages 23845–23856 (2018)Cite this article

Abstract

Soil proteomics, the large-scale characterization of the entire protein complement in soils, provides a promising approach for deciphering the role of microbial functioning in terrestrial ecosystems. However, the extraction of soil proteins in sufficient quantities and of adequate purity remains a challenging task mainly due to the co-extraction of interfering humic substances. Up to now, the treatment of soil extracts with liquid phenol has been the “gold standard” for reducing humics, while the NoviPure cleanup kit was recently launched as a non-toxic approach. The present study describes an alternative method for delivering high-purity proteins based on humic coagulation with trivalent aluminum ions (Al3+). Various experimental parameters were optimized individually in order to maximize protein yield and diminish co-extracted humics. The optimized method was applied on a set of soil samples with diverse physicochemical characteristics and a comparison with the other two techniques was conducted. The amount of residual humics resulting from Al3+-based method was 26 and 35% higher than that from phenol treatment and NoviPure Kit, respectively, but these differences were of marginal statistical significance. With regard to extracted proteins, the average yields of the three methods were comparable, without showing any statistically significant differences. Overall, humic coagulation with Al3+ offers comparable cleanup performance in terms of protein yield and purity, but it is less toxic and less complex than the phenol-partitioning method, whereas it is far less expensive than the NoviPure Kit. The new technique is expected to facilitate the implementation of proteomic studies in soils.

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Acknowledgements

This research was supported by a Marie Curie International Outgoing Fellowship (PIOF-GA-2009-235470) within the 7th European Community Framework Programme. We thank Dr. Rebecca E. Parales (University of California, Davis), for providing the Pseudomonas putida F1 strain.

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Authors and Affiliations

  1. Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Crete, Greece

    Manolis Mandalakis & Paraskevi N. Polymenakou

  2. College of Science, Northeastern University, Boston, MA, 02115, USA

    Nicolai S. Panikov & Maria V. Sizova

  3. Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany

    Aristeidis Stamatakis

Authors
  1. Manolis Mandalakis
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  2. Nicolai S. Panikov
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  3. Paraskevi N. Polymenakou
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  4. Maria V. Sizova
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  5. Aristeidis Stamatakis
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Correspondence to Manolis Mandalakis.

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Responsible editor: Zhihong Xu

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Mandalakis, M., Panikov, N.S., Polymenakou, P.N. et al. A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation. Environ Sci Pollut Res 25, 23845–23856 (2018). https://doi.org/10.1007/s11356-018-2434-z

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  • DOI: https://doi.org/10.1007/s11356-018-2434-z

Keywords

  • Soil proteins
  • Humic substances
  • Purification method
  • Coagulation
  • Soil microbes
  • Metaproteomics