NMR metabolomics for soil analysis provide complementary, orthogonal data to MIR and traditional soil chemistry approaches – a land use study

Abstract

The present study was designed to analyse soils by different methodologies to determine the range of traits that could be investigated for the study of environmental soil samples. Proton nuclear magnetic resonance spectroscopy ((1) H NMR) was employed for metametabolomic analysis of soils from agricultural systems (managed) or from soils in a native state (remnant). The metabolomic methodologies employed (grinding and extraction with sonication) are capable of breaking up cell walls and so enabled characterisation of both extracellular and intracellular components of soil. Diffuse mid-infrared spectroscopy (MIR) data was obtained for the same sample sets, and in addition, elemental composition was determined by conventional laboratory chemical testing methods. Also investigated was the antibiotic activity of the soil extracts. Resilient or suppressive soils are valued in the agricultural setting as they convey disease resistance (against bacterial and fungal pathogens) to crop plants. In order to test if any such biological activity could be detected in the soils, the extracts were tested against the bacteria Bacillus subtilis. Several extracts showed strong growth inhibition against the bacteria with the most active clustered together in principle component analysis (PCA) of the metabolomic data. The study showed that the NMR metabolomic approach corresponds more accurately to land use and biochemical properties potentially associated with suppression, while MIR data correlated well to inorganic chemical analysis. Thus, the study demonstrates the utility in combining these spectroscopic methods for soil analysis.

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control

“…PCA demonstrated that the extracts from the composts and peat clustered in a manner that was correlated with their ability to suppress Phytophthora root rot. Similarly, Rochford et al [ 60 ] observed that growth inhibition against Bacillus subtilis of different soil extracts was strongly correlated with their metabolic profile. Metabolite composition is governed by the extant microbial communities in the substrate and it is well-known that pathogen inhibition may be mediated by the secretion of antibiotics or antimicrobial compounds [ 63 , 64 ].…”

“…The metabolic approach employed here was based on water extraction followed by data acquisition by liquid chromatrography-mass spectrophotometry-HPLC-MS; although it proved to be very effective in highlighting the diversity of compost microbiome, results cannot be directly compared with previous studies, where different extraction methods were used [ 60 , 71 ]. Results we obtained are to be considered preliminary and the involvement of metabolites in the ability of composts to suppress P .…”

Community level lipid profiling of consumers as a tool for soil food web diagnostics

“…Similarly, other metabolomic studies, using techniques such as diffuse mid-infrared spectroscopy (Rochfort, Ezernieks, Kitching, & Mele, 2015) or direct infusion Fourier transform ion cyclotron resonance spectrometry (Llewellyn, Sommer, Dupont, Allen, & Viant, 2015) observed lipids to best differentiate location/habitat, whereas land use could not be separated.…”

Metabolomics: A Way Forward for Crop Improvement

“…A unique biomarker, macrocarpal was detected for Rhizoctonia solani-suppressive soil [195]. Similarly, NMR-based soil metabolic profiling was done to discriminate the suppressive and non-suppressive soils for disease resistance [196].…”