Recent years have seen unprecedented advances in our ability to gauge soil microbial diversity, yet this has not led to concomitant advances in understanding of soil processes. Much of the reason for this is that the expressed function of soil microbes is determined not only by genetic potential but also microbial physiology, substrate dynamics and diffusion. Research on substrate dynamics and in situ physiology has progressed slowly because until recently we haven’t had analytical methods capable of measuring pools and fluxes of substrates in soil, or analytical methods for profiling microbial metabolites and lipids.
We have developed mass spectrometry methods that are providing unprecedented ability to identify and quantify microbial metabolites, microbial lipids and a broad suite of substrates. Using a combination of mass spectrometry platforms we can now identify and quantify 100s of metabolites and lipids present in the soil solution and/or soil microbial biomass. This capability is providing new insights into soil function. For example, we have re-visited the age-old question of what organic N substrates are present in soil solution, and thus potentially available for uptake by microbes. In contrast to the consensus view that the pool of small organic N is dominated by 20 protein amino acids, we found that the soil solution contains > 100 N-containing compounds from 12 compound classes and some of the most abundant compounds are not protein amino acids. Other experiments have used mass spectrometry to address the question of how soil microbes cope with water deficits. We provided the first direct experimental evidence that soil microbes cope with water deficits via massive accumulation of a suite of osmolytes. The microbial osmolytes in soil, which had until now remained hidden, are globally significant and can account for an astonishing 12 gigatonnes of C that is respired by soils per year. Our mass spectrometry toolkit is also providing the first tantalising glimpses into the molecular composition of microbial lipids.