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

Gerry A. Quinn, Alyaa Abdelhameed, 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

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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, 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.

Original languageEnglish
Article number104388
Number of pages5
JournalApplied Soil Ecology
Volume173
Early online date21 Jan 2022
DOIs
Publication statusPublished online - 21 Jan 2022

Bibliographical note

Funding Information:
We thank Swansea University staff including Alun Davies, Kathryn Sinclair, Penny Diffley and Dr. Alex Griffiths-Harold, staff at Biological Mass Spectrometry Facility, Manchester University including Dr. David Knight and Dr. Julian Selley, and staff at The Ruđer Bošković Institute, Croatia, Dr. Dušica Vujaklija, Hrvoje Dagelić and Mario Strelar. The soil sampling and proteomic extraction permissions were obtained in writing from Rothamsted Research (agreement ID 13231MTA272-3). This work was supported by the Natural Environment Research Council [grant number NE/K004638/1 for G van Keulen and NE/K004212/1 for G. Peter Matthews]. Soil collection by RA, GVK, GQ and technical staff. Soil preparation by GQ in consultation with SHD, PM, GVK, IH, AG, LF, AA. Basic soil tests by GQ and Forestry commission. Soil proteomics by GQ and ED. Bioinformatics by ED, MS, GQ, AG, AA and DB. Coding by GQ and MS. Mass spectrometry by Manchester University Biological Mass Spectrometry Core Facility. Statistical consulting by DB. Manuscript writing, revision, editing and suggestions by all authors.

Funding Information:
This work was supported by the Natural Environment Research Council [grant number NE/K004638/1 for G van Keulen and NE/K004212/1 for G. Peter Matthews].

Publisher Copyright:
© 2022 The Author(s)

Keywords

  • Temperate-grasslands
  • Soil-Metaproteome
  • Protein-extraction
  • Biogeochemical-cycles
  • Regulation

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