The peptide equivalent of the 16SrRNA assay: Revealing Phylogeny and Function

Metagenomics has taught us that ocean microbes employ a diverse suite of metabolic strategies to break down complex heterogeneous particles and catalyze chemical transformations. However, to date, there has been limited success in establishing connections between microbial diversity and functions associated with subgroups of these microbes. Linking function and phylogeny is essential to developing more accurate models of the ‘microbial engines’ of ocean biogeochemical cycles, and to understanding the relationship between diversity, ecosystem stability and functional redundancy. Ecosystem modelers are now demanding higher-resolution empirical data on microbial phylogeny and physiological responses to disturbances, to help them elucidate functional redundancy on a taxonomic level (i.e., phylum, class, order, etc.).

Proteins are the only representative analyte that can resolve functional redundancy within a community of organisms by relating phylogeny and function. Unlike genes and transcripts, these dynamic macromolecules answer “who is doing what” at the time of collection, making them essential candidate biomarkers of changing chemical environments. Mass spectrometry (MS) based metaproteomics provides direct, quantitative evidence of the expression of thousands of proteins synthesized by a microbial community, the information necessary to characterize microbial responses that mitigate temporal disturbances. Our multi-disciplinary team has demonstrated that, within a metaproteome database, we can identify unique peptide sequences that resolve protein functions at different taxonomic levels. Here, we present our progress on the protein equivalent of a 16SrRNA assay, providing insight into both phylogeny and function. We integrated existing proteomics software and novel algorithms into a metaproteomics pipeline for resolving taxonomy-specific protein functions, allowing us to parameterize ecosystem processes as a function of chemistry, environment, space and time.