Environmental Exometabolomics

section of a biocrust from near Moab UT
section of a biocrust from near Moab UT
Soil is on of the most complex systems on earth, which is why it is poorly understood. It contains a large portion of the carbon pool and it is now thought that a majority of this carbon is stored in the form of microbial biomass. There can be up to 4000 microbes in just one gram of soil found through sequencing metagenomes, but what is the role of these microbes in their communities? One of our goals is to better understand the metabolites that are available in specific environments, and how they are transformed when bacteria and other microorganisms found in the ground are active. Using LC-MS, we can detect the changes in metabolites that are extractable by water, and therefore should be available to microbes in the soil, under different conditions. Knowledge of nutrient exchange will help us to maintain healthy soils.

Biological Soil Crust

Biological soil crust, or biocrusts, are topsoil microbial communities commonly found in arid regions that comprise 40% of Earth’s terrestrial surface. Essentially all metabolic activities in these systems are confined to brief periods of wetting and we have found dramatic changes in community composition that will facilitate correlation between soil microbes and metabolites.1 Microcoleus vaginatus, a filamentous cyanobacteria, is the main component of these biocrusts. It can stabilize the soil and retains water in its polysaccharide sheath. In a recent paper by Baran et al 2, we found that the Microcoleus seems to mediate a large portion of the metabolite exchange because it is not selective in the metabolites it takes up and releases, whereas other heterotrophs in the same environment are much more selective. It is predicted that as biocrusts age, Microcoleus vaginatus may be replaced with a similar species, Microcoleus steenstrupii. We plan to study the differences between these two strains’ exometabolic profiles to understand how this may affect the community structure.

Desert biocrusts can be collected in a dormant desiccated state for laboratory wetting events on essentially intact soil communities. They can be stored in this state for years enabling follow-on detailed studies to make and test predictions making this a simple ‘test bed’ needed for developing and testing exometabolomics approaches.

Angelo Coast Range Reserve

The Angelo Coast Range Reserve is located in Northern California and is used for a variety of research projects at the University of California – Berkeley, including one that is attempting to study how the structure of the soil changes due to differences in rainfall volume and duration – major factors affecting soil fertility. Our goal is to understand how these rainfall patterns affect the metabolites that is available to the microbes at different depths of the soil and how this may influence the microbial community. In a collaboration with Jill Banfield’s Lab at UC Berkeley, we are sampling the site before and after rain events to correlate the changes in metagenomes which represent the community composition with the metabolites that are used and converted to try to understand the roles that the individual classes of microbes play in the overall community.

(1) Rajeev, L. et al (2013). Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. The ISME Journal. 7, 2178–2191. doi:10.1038/ismej.2013.83
(2) Baran, R. et al (2015) Exometabolite niche partitioning among sympatric soil bacteria. Nature Comm. 6, 8289. doi:10.1038/ncomms9289