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Soil microbiome pH perturbation metabolomics - LC

ABSTRACT: Examined soil microbiome microcosms to determine the effect of changing pH on the production of lignocellulolytic enzymes. Soil from a Prosser, Washington field site was incubated in mesh bags on top of a soil interfacing glass bead matrix with MOPS minimal media amended with or without carboxymethyl cellulose at three different pH levels. After incubation, 2 mL of media solution was collected, centrifuged, and filtered to remove cells prior to preparing supernatant for metabolomics. For data generated, confident metabolite identifications are made using Thermo Compound Discoverer 3.3. For RP and HILIC positive and negative mode, spectra are aligned using an adaptive curve with a maximum of 0.3 or 0.6 RT shift respectively and a 3 ppm mass tolerance. Peaks are selected based on a minimum intensity of 1e6 and a chromatographic S/N of 3. Detected features are grouped based on a mass tolerance of 3 ppm and a RT tolerance of 0.3. Features are then filtered out depending on the number of samples. Compounds are assigned based on Isotopic pattern, RT, MS1, and/or MS2. All identifications and integrated peaks are manually validated and exported for statistical analysis. We provide, on average, four levels of identification starting from the most to least confidence: 1. Match with MS1, MS2, AND RT; 2. Match with MS2 only; 3. Match with MS1 and RT; 4. Match primarily with MS1 and partial MS2 match.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Environmental Samples <bacteria> (ncbitaxon:48479)

SUBMITTER: Ryan S. McClure Nicholas J. Reichart

PROVIDER: MSV000100842 | MassIVE | Fri Feb 13 10:28:00 GMT 2026

REPOSITORIES: MassIVE

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