13C-Isotopomer-based metabolomics of microbial groups isolated from two forest soils

Soil microorganisms are the primary mediators of organic matter decomposition and humification processes in soil, which represent a critical C flux in the global C cycle. Little is known about how soil microbes regulate carbon cycling including the contribution of their own biomass to stable soil organic matter. A comprehensive understanding of microbial composition is a first step to unraveling microbial regulation of soil humification processes. For this purpose, we isolated 23 microbial strains representing four major groups (Gram (+) bacteria, Gram (−) bacteria, Actinobacteria, and Fungi) from a temperate and a tropical forest soil. The microbial isolates were cultured with uniformly ¹³C-labeled glucose as the C source such that all biochemical components synthesized from glucose were ¹³C labeled. This approach enabled field mesocosm experiments on tracking microbial decomposition, while facilitating solution- and solid-state NMR analysis of microbial composition. Polar and lipid extracts of labeled biomass of the four microbial groups from the two forest sites were profiled by 2D NMR methods, including high-resolution heteronuclear single quantum coherence spectroscopy and HCCH-total correlation spectroscopy. This ¹³C labeling approach also enabled the analysis of intact biomass by 2D solid-state ¹³C–¹³C correlation spectroscopy. Distinction between microbial groups and sites was observed in the polar and lipophilic metabolite profiles. Dominant differences could also be related to the capacity for lipid β-oxidation or adaptation to desiccation. Solid-state NMR further revealed differential synthetic capacity for glycolipids among groups. This technology coupled with ¹³C metabolite profiling should facilitate future functional annotation of indigenous microbial genomes.