MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments

Area of Science:

• Environmental chemistry
• Analytical chemistry
• Microbiology

Background:

• Metabolites are crucial for microbial community functions like nutrient exchange and communication.
• Analyzing metabolites in hypersaline samples via liquid chromatography-mass spectrometry (LC-MS) is challenging due to high salt concentrations.
• Existing desalting methods are often ineffective for samples with extreme salt loads.

Purpose of the Study:

• To develop a facile method for direct LC-MS-based exometabolomics analysis of hypersaline samples.
• To enable the detection and quantification of metabolites and chemicals in matrices up to 2 M total dissolved salts.
• To provide a versatile tool applicable to both targeted and untargeted metabolomics.

Main Methods:

• Developed MetFish, a method employing in situ chemical derivatization followed by extraction.
• Applied MetFish to molecules with amine, carboxylic acid, carbonyl, or hydroxyl functional groups.
• Integrated MetFish into targeted and untargeted analysis workflows for mass spectrometry.

Main Results:

• MetFish achieved limits of quantification as low as 1 nM in targeted analyses.
• Demonstrated broad linear dynamic ranges (5-6 orders of magnitude) with excellent linearity and low interday reproducibility (median 2.6%).
• Successfully applied MetFish to analyze microbial consortia, prairie soil, and hydraulic fracturing fluids, revealing exometabolome dynamics.

Conclusions:

• MetFish overcomes matrix effects in hypersaline samples, enabling direct mass spectrometry-based metabolomics.
• The method is sensitive, accurate, and versatile for diverse hypersaline environments.
• Facilitates novel insights into microbial community functions and chemical dynamics in extreme conditions.