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Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome

Gerry Quinn, Alyaa Abdel Hameed, Ibrahim M. Banat, Daniel Berrar, Stefan Doerr Orcid Logo, Ed Dudley, Lewis Francis Orcid Logo, Salvatore Gazze, Ingrid Hallin, G. Peter Matthews, Martin T. Swain, W. Richard Whalley, Geertje Van Keulen Orcid Logo

Applied Soil Ecology, Volume: 173, Start page: 104388

Swansea University Authors: Gerry Quinn, Alyaa Abdel Hameed, Stefan Doerr Orcid Logo, Ed Dudley, Lewis Francis Orcid Logo, Salvatore Gazze, Geertje Van Keulen Orcid Logo

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DOI (Published version): 10.1016/j.apsoil.2022.104388

Abstract

Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, th...

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Published in: Applied Soil Ecology
ISSN: 0929-1393
Published: Elsevier BV 2022
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URI: https://cronfa.swan.ac.uk/Record/cronfa59232
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The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically fraught process due to difficulties with co-extraction of humic material and lack of compatible databases to identify proteins. To address these issues, we combined two protein extraction techniques on Park Grass experiment soil, one based on humic acid removal, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracts humic material, namely an established surfactant method. A broad range of proteins were identified by matching the mass spectra of extracted soil proteins against a tailored Park Grass proteome database. These were mainly in the categories of &#x201C;protein metabolism&#x201D;, &#x201C;membrane transport&#x201D;, &#x201C;carbohydrate metabolism&#x201D;, &#x201C;respiration&#x201D; &#x201C;ribosomal and nitrogen cycle&#x201D; proteins, enabling reconstitution of specific processes in grassland soil. Protein annotation using NCBI and EBI databases inferred that the Park Grass soil is dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phylum level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to connect protein identities to regulatory and signalling networks of key biogeochemical cycles, notably the nitrogen cycle. 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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language><licence>http://creativecommons.org/licenses/by/4.0/</licence></document></documents><OutputDurs/></rfc1807>
spelling 2022-05-27T10:51:49.9249189 v2 59232 2022-01-24 Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome 9e13315f1b5839f9a90a47103130261b Gerry Quinn Gerry Quinn true false 676df49a2baf58320d463fa023063787 Alyaa Abdel Hameed Alyaa Abdel Hameed true false 575eb5094f2328249328b3e43deb5088 0000-0002-8700-9002 Stefan Doerr Stefan Doerr true false c7d05f992a817cd3b9a5f946bd909b71 Ed Dudley Ed Dudley true false 10f61f9c1248951c1a33f6a89498f37d 0000-0002-7803-7714 Lewis Francis Lewis Francis true false 586f1f49652b97c5c3ab99a45a1c58bf Salvatore Gazze Salvatore Gazze true false 6b2c798924ac19de63e2168d50b99425 0000-0002-6044-1575 Geertje Van Keulen Geertje Van Keulen true false 2022-01-24 PMSC Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically fraught process due to difficulties with co-extraction of humic material and lack of compatible databases to identify proteins. To address these issues, we combined two protein extraction techniques on Park Grass experiment soil, one based on humic acid removal, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracts humic material, namely an established surfactant method. A broad range of proteins were identified by matching the mass spectra of extracted soil proteins against a tailored Park Grass proteome database. These were mainly in the categories of “protein metabolism”, “membrane transport”, “carbohydrate metabolism”, “respiration” “ribosomal and nitrogen cycle” proteins, enabling reconstitution of specific processes in grassland soil. Protein annotation using NCBI and EBI databases inferred that the Park Grass soil is dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phylum level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to connect protein identities to regulatory and signalling networks of key biogeochemical cycles, notably the nitrogen cycle. The newly identified Park Grass metaproteome thus provides a baseline on which future targeted studies of important soil processes and their control can be built. Journal Article Applied Soil Ecology 173 104388 Elsevier BV 0929-1393 Temperate-grasslands, Soil-Metaproteome, Protein-extraction, Biogeochemical-cycles, Regulation 1 5 2022 2022-05-01 10.1016/j.apsoil.2022.104388 COLLEGE NANME Medicine COLLEGE CODE PMSC Swansea University External research funder(s) paid the OA fee (includes OA grants disbursed by the Library) NERC NE/K004638/1, NE/K004212/1 2022-05-27T10:51:49.9249189 2022-01-24T18:03:07.3466868 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Gerry Quinn 1 Alyaa Abdel Hameed 2 Ibrahim M. Banat 3 Daniel Berrar 4 Stefan Doerr 0000-0002-8700-9002 5 Ed Dudley 6 Lewis Francis 0000-0002-7803-7714 7 Salvatore Gazze 8 Ingrid Hallin 9 G. Peter Matthews 10 Martin T. Swain 11 W. Richard Whalley 12 Geertje Van Keulen 0000-0002-6044-1575 13 59232__22252__59ac2d92e0bc4837b3eb927df4203b30.pdf 59232.VOR.pdf 2022-01-31T14:27:47.4586984 Output 2578069 application/pdf Version of Record true Copyright: The Authors. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. true eng http://creativecommons.org/licenses/by/4.0/
title Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
spellingShingle Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
Gerry Quinn
Alyaa Abdel Hameed
Stefan Doerr
Ed Dudley
Lewis Francis
Salvatore Gazze
Geertje Van Keulen
title_short Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
title_full Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
title_fullStr Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
title_full_unstemmed Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
title_sort Complementary protein extraction methods increase the identification of the Park Grass Experiment metaproteome
author_id_str_mv 9e13315f1b5839f9a90a47103130261b
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author_id_fullname_str_mv 9e13315f1b5839f9a90a47103130261b_***_Gerry Quinn
676df49a2baf58320d463fa023063787_***_Alyaa Abdel Hameed
575eb5094f2328249328b3e43deb5088_***_Stefan Doerr
c7d05f992a817cd3b9a5f946bd909b71_***_Ed Dudley
10f61f9c1248951c1a33f6a89498f37d_***_Lewis Francis
586f1f49652b97c5c3ab99a45a1c58bf_***_Salvatore Gazze
6b2c798924ac19de63e2168d50b99425_***_Geertje Van Keulen
author Gerry Quinn
Alyaa Abdel Hameed
Stefan Doerr
Ed Dudley
Lewis Francis
Salvatore Gazze
Geertje Van Keulen
author2 Gerry Quinn
Alyaa Abdel Hameed
Ibrahim M. Banat
Daniel Berrar
Stefan Doerr
Ed Dudley
Lewis Francis
Salvatore Gazze
Ingrid Hallin
G. Peter Matthews
Martin T. Swain
W. Richard Whalley
Geertje Van Keulen
format Journal article
container_title Applied Soil Ecology
container_volume 173
container_start_page 104388
publishDate 2022
institution Swansea University
issn 0929-1393
doi_str_mv 10.1016/j.apsoil.2022.104388
publisher Elsevier BV
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
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description Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically fraught process due to difficulties with co-extraction of humic material and lack of compatible databases to identify proteins. To address these issues, we combined two protein extraction techniques on Park Grass experiment soil, one based on humic acid removal, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracts humic material, namely an established surfactant method. A broad range of proteins were identified by matching the mass spectra of extracted soil proteins against a tailored Park Grass proteome database. These were mainly in the categories of “protein metabolism”, “membrane transport”, “carbohydrate metabolism”, “respiration” “ribosomal and nitrogen cycle” proteins, enabling reconstitution of specific processes in grassland soil. Protein annotation using NCBI and EBI databases inferred that the Park Grass soil is dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phylum level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to connect protein identities to regulatory and signalling networks of key biogeochemical cycles, notably the nitrogen cycle. The newly identified Park Grass metaproteome thus provides a baseline on which future targeted studies of important soil processes and their control can be built.
published_date 2022-05-01T04:16:23Z
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