Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights
Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptom...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/22/8455 |
| _version_ | 1797548277947695104 |
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| author | Maria Tartaglia Felipe Bastida Rosaria Sciarrillo Carmine Guarino |
| author_facet | Maria Tartaglia Felipe Bastida Rosaria Sciarrillo Carmine Guarino |
| author_sort | Maria Tartaglia |
| collection | DOAJ |
| description | Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil. |
| first_indexed | 2024-03-10T14:57:02Z |
| format | Article |
| id | doaj.art-9301626c51f34e27a1746f6d41cf1667 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T14:57:02Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-9301626c51f34e27a1746f6d41cf16672023-11-20T20:31:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-11-012122845510.3390/ijms21228455Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological InsightsMaria Tartaglia0Felipe Bastida1Rosaria Sciarrillo2Carmine Guarino3Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, ItalyCEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, SpainDepartment of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, ItalyDepartment of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, ItalySoil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.https://www.mdpi.com/1422-0067/21/22/8455soil metaproteomicsprotein extractionrhizosphere crosstalkpolluted soil |
| spellingShingle | Maria Tartaglia Felipe Bastida Rosaria Sciarrillo Carmine Guarino Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights International Journal of Molecular Sciences soil metaproteomics protein extraction rhizosphere crosstalk polluted soil |
| title | Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights |
| title_full | Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights |
| title_fullStr | Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights |
| title_full_unstemmed | Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights |
| title_short | Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights |
| title_sort | soil metaproteomics for the study of the relationships between microorganisms and plants a review of extraction protocols and ecological insights |
| topic | soil metaproteomics protein extraction rhizosphere crosstalk polluted soil |
| url | https://www.mdpi.com/1422-0067/21/22/8455 |
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