Assessing the impact of interfering organic matter on soil metaproteomic workflow

M. Waibel, K. McDonnell, M. Tuohy, S. Shirran, S. Synowsky, B. Thornton, E. Paterson, F. Brennan, F. Abram*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Soil organic matter (SOM) is biologically, chemically, and physically complex. As a major store of nutrients within soil, it plays an important role in nutrient provision to plants. An enhanced understanding of SOM utilisation processes could underpin better fertiliser management for plant growth, with reduced environmental losses. Metaproteomics can allow the characterisation of protein profiles and could help gaining insights into SOM microbial decomposition mechanisms. Here, we applied three different extraction methods to two soil types to recover SOM with different characteristics. Specifically, water extractable organic matter, mineral associated organic matter and protein-bound organic matter were targeted with the aim to investigate the metaproteome enriched in those extractions. As a proof-of-concept replicated extracts from one soil were further analysed for peptide identification using liquid chromatography followed by tandem mass spectrometry. We employ a framework for mining mass spectra for both peptide assignment and fragmentation pattern characterisation. Different extracts were found to exhibit contrasting total protein and humic substance content for the two soils investigated. Overall, water extracts displayed the lowest humic substance content (in both soils) and the highest number of peptide identifications (in the soil investigated) with most frequent peptide hits associated with diverse substrate/ligand binding proteins of Proteobacteria and derived taxa. Our framework also highlighted a strong peptidic signal in unassigned and unmatched spectra, information that is currently not captured by the pipelines employed in this study. Taken together, this work points to specific areas for optimisation in chromatography and mass spectrometry to adequately characterise SOM associated metaproteomes.
Original languageEnglish
Article numbere13392
Number of pages14
JournalEuropean Journal of Soil Science
Issue number3
Early online date22 Jun 2023
Publication statusPublished - 22 Jun 2023


  • Soil organic matter
  • Chemical fractionation
  • Metaproteomics
  • Grassland soil


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