Extraction methods for untargeted metabolomics influence enzymatic activity in diverse soils

Madison A Bell; Ulrica McKim; Amanda Sproule; Ryan Tobalt; Edward Gregorich; David P Overy

doi:10.1016/j.scitotenv.2022.154433

Extraction methods for untargeted metabolomics influence enzymatic activity in diverse soils

Sci Total Environ. 2022 Jul 1:828:154433. doi: 10.1016/j.scitotenv.2022.154433. Epub 2022 Mar 8.

Authors

Madison A Bell¹, Ulrica McKim², Amanda Sproule², Ryan Tobalt², Edward Gregorich³, David P Overy⁴

Affiliations

¹ Agriculture and Agri-food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; Laboratory for the Analysis of Natural and Synthetic Environmental Toxicants, Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
² Agriculture and Agri-food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada.
³ Agriculture and Agri-food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada. Electronic address: ed.gregorich@agr.gc.ca.
⁴ Agriculture and Agri-food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada. Electronic address: david.overy@agr.gc.ca.

PMID: 35276180
DOI: 10.1016/j.scitotenv.2022.154433

Abstract

Soil organic matter (SOM) is the largest carbon pool in terrestrial ecosystems and underpins the health and productivity of soil. Accurate characterization of its chemical composition will improve our understanding of biotic and abiotic processes regulating its stabilization. Our purpose in this study was to estimate the loss of SOM by microbial and exoenzymatic activity that might occur when soil is extracted for analysis of representative low molecular weight mass features using untargeted metabolomics. Two mined clays (kaolinite, montmorillonite) and three diverse soils (varying in texture, specific surface area and cation exchange capacity) were used to assess the extraction efficiency and loss of three enzymatic activity indicators (2,6-dichloroindophenol sodium salt hydrate [DCIP], 4-methylumbelliferyl phosphate [MUBph] and 3,4-dihydroxy-L-phenylalanine [LDOPA]) during extraction with two different solvents (water and methanol). Losses of the indicators were attributed to extraction method (ultrasonication, shaking, or shaking following chloroform fumigation), physical properties associated with the soil/clay type, and microbial activity. Soil/clay type strongly influenced indicator recovery and hence, SOM recovery. Choice of extraction method strongly influenced the composition and recovery of representative SOM mass features, while the choice of solvent determined whether the soil type or extraction method had a greater influence of compositional differences in the SOM mass features extracted. Extraction following chloroform fumigation had the greatest loss of the indicators, due to enzymatic activity and/or adsorption onto the soil matrix. Minimal variation in composition and loss of SOM mass features occurred during extraction by shaking for the soils tested; we therefore recommend it as the method of choice for untargeted SOM extraction studies.

Keywords: Enzymatic activity; Extraction methods; Extraction solvents; Soil organic matter; Untargeted metabolomics.

MeSH terms

Chloroform
Clay
Ecosystem*
Metabolomics
Soil* / chemistry
Solvents / chemistry

Substances

Soil
Solvents
Chloroform
Clay