Microbial volatile organic compounds: important but overlooked in microbial systems studies

Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic substrates and products and as signaling molecules. Yet, current microbial metabolomic studies predominantly focus on nonvolatile metabolites and overlook VOCs, which therefore represent a missing component of the metabolome. In metabolomic studies, it is important to know which compounds within metabolic pathways may be considered volatile to predict potentially overlooked compounds and potentially include VOC measurement approaches to capture them.

In this study, we adapted and automated an atmospheric vapor pressure predictive model for metabolomic research to calculate relative volatility indices (RVIs) for compounds in a metabolic pathway through identification of the compound’s functional groups. We then evaluated the importance of considering compound volatility in soil metabolomic studies by comparing the ability of a suite of complementary analytical tools (nuclear magnetic resonance (NMR) spectroscopy, gas chromatography-mass spectrometry (GC-MS), and Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS)) to capture complete metabolic pathways in soil.

We found that the metabolites that were not detected by NMR, GC-MS, and FT-ICR-MS within metabolic pathways had significantly higher volatility than those that were detected, revealing a bias against volatile metabolites in standard metabolomics pipelines. Moreover, we show that including VOC-resolving measurements (proton transfer reaction time of flight mass spectrometry (PTR-TOF-MS)) captured the volatile compounds missed by other metabolomic techniques, and together, the combined approaches captured more complete microbial metabolic processes in soil.  Our results demonstrate the importance and prevalence of VOCs as metabolites in soil. Including volatile metabolites in metabolomics, both conceptually and in practice, will build a more comprehensive understanding of microbial processes across ecological communities.