Abstract
Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea. Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.
Highlights
Chronic and directional environmental drivers such as nutrient and organic matter enrichment are causing state changes in many ecosystems (Rabalais et al 2009, Scheffer 2009)
The taxonomic composition of bacteria contributing to protein expression in our study, and in our metagenome, is consistent with findings of previous studies of bacterial communities in Sarracenia species
One genomic study of Sarracenia alata pitcher bacterial communities revealed an abundance of Proteobacteria
Summary
Chronic and directional environmental drivers such as nutrient and organic matter enrichment are causing state changes in many ecosystems (Rabalais et al 2009, Scheffer 2009) Mitigating or preventing these state changes requires predicting them with sufficient lead-time (Biggs et al 2009). As a first step toward determining the utility of microbial protein biomarkers as early warning signals of state changes, we conducted an environmental proteomics screen of the aquatic ecosystem in S. purpurea pitchers enriched with organic matter to determine whether there are detectable differences between the proteins, associated molecular pathways, and taxa contributing to expressed proteins in microbial (nonviral organisms
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