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Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives

Bastida, F.; Moreno, J. L.; Cuevas, César Nicolás LU ; Hernandez, T. and Garcia, C. (2009) In European Journal of Soil Science 60. p.845-859
Abstract
Soil is a dynamic system in which microorganisms perform important tasks in organic matter transformations and nutrient cycles. Recently, some studies have started to focus on soil metaproteomics as a tool for understanding the function and the role of members of the microbial community. The aim of our work was to provide a review of soil proteomics by looking at the methodologies used in order to illustrate the challenges and gaps in this field, and to provide a broad perspective about the use and meaning of soil metaproteomics. The development of soil metaproteomics is influenced strongly by the extraction methods. Several methods are available but only a few provide an identification of soil proteins, while others extract proteins and... (More)
Soil is a dynamic system in which microorganisms perform important tasks in organic matter transformations and nutrient cycles. Recently, some studies have started to focus on soil metaproteomics as a tool for understanding the function and the role of members of the microbial community. The aim of our work was to provide a review of soil proteomics by looking at the methodologies used in order to illustrate the challenges and gaps in this field, and to provide a broad perspective about the use and meaning of soil metaproteomics. The development of soil metaproteomics is influenced strongly by the extraction methods. Several methods are available but only a few provide an identification of soil proteins, while others extract proteins and are able to separate them by electrophoresis but do not provide an identification. The extraction of humic compounds together with proteins interferes with the latter's separation and identification, although some methods can avoid these chemical interferences. Nevertheless, the major problems regarding protein identification reside in the fact that soil is a poor source of proteins and that there is not enough sequence-database information for the identification of proteins by mass spectrometric analysis. Once these pitfalls have been solved, the identification of soil proteins may provide information about the biogeochemical potential of soils and pollutant degradation and act as an indicator of soil quality, identifying which proteins and microorganisms are affected by a degradation process. The development of soil metaproteomics opens the way to proteomic studies in other complex substrates, such as organic wastes. These studies can be a source of knowledge about the possibility of driven soil restoration in polluted and degraded areas with low organic matter content and even for the identification of enzymes and proteins with a potential biotechnological value. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
polyacrylamide-gel electrophoresis, microbial community structure, enzyme-activities, organic-matter, sewage-sludge, mass-spectrometry, proteome analysis, nmr-spectroscopy, plant-tissues, extraction
in
European Journal of Soil Science
volume
60
pages
845 - 859
publisher
Wiley-Blackwell
external identifiers
  • scopus:73149103678
ISSN
1365-2389
DOI
10.1111/j.1365-2389.2009.01184.x
language
English
LU publication?
no
id
a5644324-b4cc-4509-9dfc-ac8fcdd309cd (old id 4362829)
date added to LUP
2014-03-26 13:38:36
date last changed
2017-07-30 04:48:38
@article{a5644324-b4cc-4509-9dfc-ac8fcdd309cd,
  abstract     = {Soil is a dynamic system in which microorganisms perform important tasks in organic matter transformations and nutrient cycles. Recently, some studies have started to focus on soil metaproteomics as a tool for understanding the function and the role of members of the microbial community. The aim of our work was to provide a review of soil proteomics by looking at the methodologies used in order to illustrate the challenges and gaps in this field, and to provide a broad perspective about the use and meaning of soil metaproteomics. The development of soil metaproteomics is influenced strongly by the extraction methods. Several methods are available but only a few provide an identification of soil proteins, while others extract proteins and are able to separate them by electrophoresis but do not provide an identification. The extraction of humic compounds together with proteins interferes with the latter's separation and identification, although some methods can avoid these chemical interferences. Nevertheless, the major problems regarding protein identification reside in the fact that soil is a poor source of proteins and that there is not enough sequence-database information for the identification of proteins by mass spectrometric analysis. Once these pitfalls have been solved, the identification of soil proteins may provide information about the biogeochemical potential of soils and pollutant degradation and act as an indicator of soil quality, identifying which proteins and microorganisms are affected by a degradation process. The development of soil metaproteomics opens the way to proteomic studies in other complex substrates, such as organic wastes. These studies can be a source of knowledge about the possibility of driven soil restoration in polluted and degraded areas with low organic matter content and even for the identification of enzymes and proteins with a potential biotechnological value.},
  author       = {Bastida, F. and Moreno, J. L. and Cuevas, César Nicolás and Hernandez, T. and Garcia, C.},
  issn         = {1365-2389},
  keyword      = {polyacrylamide-gel electrophoresis,microbial community structure,enzyme-activities,organic-matter,sewage-sludge,mass-spectrometry,proteome analysis,nmr-spectroscopy,plant-tissues,extraction},
  language     = {eng},
  pages        = {845--859},
  publisher    = {Wiley-Blackwell},
  series       = {European Journal of Soil Science},
  title        = {Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives},
  url          = {http://dx.doi.org/10.1111/j.1365-2389.2009.01184.x},
  volume       = {60},
  year         = {2009},
}