Determination of Soil Organic Matter Composition and Bacterial Cycling Using Soil Metabolomic Approaches.

Microbial mineralization of soil organic matter (SOM) is a key determinant of global biogeochemical cycles of carbon and nitrogen, however, the chemical composition and cycling of SOM by specific soil bacteria are poorly understood.  Mass spectrometry based metabolomic methods have the potential to resolve these chemical components and help link their cycing to microbial community composition, improving our understanding of carbon cycling in soils. Here, we describe liquid chromatography coupled to tandem mass spectrometry approaches for the untargeted metabolite profiling of soil metabolites and examination of the activities of soil isolate bacteria against these metabolites.  This was accomplished by culturing soil isolates in complex media prepared from soil extracts and using exometabolite profiling to compare the spent vs. fresh media to detect depletion or production of metabolites. Importantly, these soil extracts contain previously uncharacterized metabolites which may be relevant under environmental conditions.

Our soil metabolomics methods detected hundreds of metabolites from soils from which we identified a set of metabolites, including disaccharides, that were uptaken by essentially all studied isolates suggesting a potential competition for these compounds in the soil. Beyond these few metabolites, the individual heterotrophs examined showed specialization towards specific metabolites. Surprisingly, many of the most abundant oligosaccharides and other metabolites were ignored by these isolates. This observation that soil heterotrophs target specific SOM components is counter to conventional thinking of soil heterotrophs as ‘generalists’. Rather it may be that heterotrophs are highly specialized to use specific metabolites and SOM composition may play a significant role in determining community structure. Therefore, the observed complexity of soil SOM composition may explain some portion of the tremendous diversity of soil microbes. 

 

We gratefully acknowledge funding from the ENIGMA (http://enigma.lbl.gov), DOE Early Career and Carbon Cycling Programs at LBNL all supported by the Office of Biological and Environmental Research at the US Department of Energy Contract No: DE-AC02-05CH11