Marine metabolomics: a method for the non-targeted measurement of metabolites in seawater by gas-chromatography mass spectrometry

All life exchanges molecules with its environment. While these metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats has hampered quantitative analyses of the ocean metabolome. To overcome these limitations, we developed SeaMet, a gas chromatography-mass spectrometry (GC-MS) method that detects hundreds of metabolites down to nano-molar concentrations in less than one milliliter of seawater. Using a set of metabolites dissolved in artificial seawater to benchmark our method, we show metabolite signal detection increased on average across ions by 324 fold in comparison to standard GC-MS methods. Our observed signal improvement occurred across tested metabolite classes and provides reproducible and quantifiable results. To showcase the capabilities of our method, we used SeaMet to explore the production and consumption of metabolites during culture of a heterotrophic bacteria that is widespread in the North Sea. Our approach revealed successional uptake of amino acids, while sugars were not consumed, and highlight the power of metabolomics in providing insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered a remarkable diversity and abundance of sugars and fatty acids, compounds predicted to be rapidly consumed by marine microorganisms. Our method advances marine metabolomics by enabling the unbiased, and quantitative analysis of marine metabolites, and will help provide new insights into carbon cycle dynamics and ocean biogeochemistry. SignificanceMetabolites are the chemical currency of cellular metabolism across all domains of life. However, describing metabolites that occur in the oceans is lagging behind similar studies conducted on land. The central challenge in marine metabolomics is that salt prevents the comprehensive analysis of metabolites in seawater. We developed a method, SeaMet, that overcomes the limitations of salt on metabolite detection. SeaMet provides a time and cost efficient method, using gas chromatography-mass spectrometry, for the reproducible identification and quantification of a broad range of marine compounds. Considering the oceans contain the largest organic carbon pool on Earth, describing the marine metabolome is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage.