Metaproteomic survey reveals differences in composition and function between microbial communities in detritus-enriched and unmanipulated ecosystems
Eutrophication of aquatic ecosystems due to nutrient and detrital enrichment is expected to occur more frequently as climate and land use change. It is important to develop early warning indicators to predict eutrophication because it is difficult to manage once it occurs. Current generic prediction methods rely on detecting changes in statistical parameters of the time series of state variables such as sediment diatom composition, turbidity, and vegetation cover; however, these indicators may not offer enough lead-time for successful mitigation. Microbial breakdown of detritus underlies eutrophication and often initiates changes in traditionally measured state variables of aquatic systems. Therefore, molecular indicators based on these underlying microbial processes may allow more lead-time than traditional indicators. As a critical first step in identifying these microbial processes, we developed and conducted a metaproteomic survey to identify microbial composition and function in ambient control and experimentally enriched natural aquatic ecosystems contained within pitchers of the Northern Pitcher Plant (Sarracenia purpurea). We enriched replicate pitchers in the field with detritus (arthropod prey) and used shotgun metaproteomics and a custom translated metagenomic database to compare expressed proteins, molecular pathways, and microbial taxa in enriched pitchers to pitchers that experienced ambient prey capture.
Enriched and ambient control pitchers differed in both microbial composition and function. Both enriched and control pitchers housed similar numbers of bacterial classes; however, taxonomic evenness was substantially higher in control pitchers (PIE=0.66) than in enriched pitchers (PIE=0.31). Betaproteobacteria was the most abundant bacterial class in both enriched and control pitchers, but Betaproteobacteria were more prevalent in enriched pitchers (83%) than in control pitchers (51%). Aerobic bacteria dominated control pitchers (77%) while facultative aerobic bacteria dominated enriched pitchers (62%). Sixteen metabolic pathways, including fatty acid biosynthesis, pyruvate metabolism, citrate cycle, and glyoxylate and dicarboxylate metabolism, were over-represented in the control pitchers. Nine pathways, including fatty acid degradation and propanoate metabolism, were over-represented in the enriched pitchers. We show that proteomic composition and metabolic function differ between enriched and control pitchers. Our efficient metaproteomic pipeline makes it possible to rapidly survey for molecular early warning indicators of state changes initiated by nutrient and detrital enrichment. Because such indicators are derived from microbial processes that occur at the detrital base of aquatic food webs, they may be directly applicable to other enriched aquatic ecosystems.