Ecological and metabolic interactions of microbial communities defined by metaproteomics

Metaproteomic studies of microbial communities from environmental samples have rapidly increased in recent years due to many technological advances in mass spectrometry (MS). These approaches allow for an investigation into the physiology of organisms within natural settings, opening the door to understanding metabolic responses in situ. We have collected whole community proteomes of microbial communities from extreme environments (i.e., Acid Mine Drainage [AMD] biofilms) and from coastal seawater ecosystems, with the goal of defining community interactions and physiological changes across environmental gradients and experimental treatments. Studies within the AMD system have shown that the proteome of the dominant population within this system is relatively stable despite environmental fluctuations, and changes in its metabolism correlate with community diversification and ecological succession within biofilms. Based on the observed metabolic differences, we infer that these changes are the likely result of competitive interactions within the biofilm and growth rate changes within this population. We have extended this approach to study marine microbial communities by developing a new method that combines stable isotope probing with MS-proteomics (Proteomics-SIP). This technique allows resource assimilation to be tracked across multiple populations within microbial communities in addition to investigating the in situ physiology of organisms. Clear differences have been observed between the label enrichment and physiology of dominant populations from this environment. These studies are beginning to provide insight into the resource preferences of the major taxa comprising these communities, the resource acquisition strategies used by each group, and overall population dynamics within these systems as resources change.