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

Microbial communities exchange molecules with their environment that play a major role in global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats has hampered non-targeted analyses of the ocean exo-metabolome. To overcome these limitations, we developed SeaMet, a gas chromatography-mass spectrometry (GC-MS) method that detects at minimum 107 metabolites down to nano-molar concentrations in less than one milliliter of seawater, and improves signal detection by 324 fold compared to standard methods for marine samples. To showcase the strengths of SeaMet, we used it to explore marine metabolomes in vitro and in vivo. For the former, we measured the production and consumption of metabolites during culture of a heterotrophic bacterium 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 exocellular metabolomics in providing insights into nutrient uptake and energy conservation in marine microorganisms. For in vivo analyses, we 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 high concentrations of many different sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral-reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a non-targeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans. Importance The non-targeted, hypothesis-free approach using metabolomics to analyzing metabolites that occur in the oceans is less developed than for terrestrial and limnic ecosystems. The central challenge in marine metabolomics is that salt prevents the comprehensive analysis of metabolites in seawater. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering the oceans contain the largest organic carbon pool on Earth, describing the marine metabolome using non-targeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other ‘omics’ (e.g., genomics, transcriptomics and proteomics) level approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.