Identifying Specific Preferences in Organic Compound Consumption by Desert Soil Microbes


Every natural soil ecosystem hosts a great diversity of microbes that consume complex organic matter and transform it to simpler small carbon compounds (metabolites) or gaseous endproducts such as carbon dioxide. This decompositional microbial activity transforms organic compounds in the soil, playing a critical role in the global carbon cycle. To determine the functional characteristics of a microbial community’s different members, it is necessary to understand the complex mixture of metabolites present in their environment and to determine which compounds are preferentially consumed by each microorganism. Researchers at Lawrence Berkeley National Laboratory and collaborating institutions have used new exometabolomics techniques to quantitatively analyze the compounds consumed by seven bacterial species isolated from soil crusts in the desert environment of the Colorado Plateau. In these arid environments, most of the organic matter is produced by photosynthetic bacteria and released in the form of metabolites that other microbes can consume and further transform. The investigators discovered that each of the seven species consumes only 13% to 26% of the nearly 500 metabolites produced by these bacteria, and only 0.4% of the metabolites are used by all of them. These different feeding habits may represent a form of ecological niche specialization and may play important roles in maintaining non-overlapping diversity within microbial consortia. This study constitutes a significant advance in our understanding of how microbes in terrestrial ecosystems transform soil organic matter and may affect atmospheric carbon dioxide levels.


Baran, R., E. Brodie, J. Mayberry-Lewis, E. Hummel, U. N. Da Rocha, R. Chakraborty, B. Bowen, U. Karaoz, H. Cadillo-Quiroz, F. Garcia-Pichel, and T. Northen. 2015. “Exometabolite Niche Partitioning Among Sympatric Soil Bacteria,” Nature Communications 6(8289), DOI:10.1038/ncomms9289.