Microbes are the most abundant organisms on the planet in terms of biomass, containing ~5,000 times the amount of carbon found in the entire human population. A single teaspoon of ocean water often contains over 1 million individual microbial cells. Given limited differences in size and shape, distinguishing one species from another under the microscope is difficult. Associating specific functions with individual cells or populations is even more challenging. Marine microbes drive biogeochemical cycles of carbon, nitrogen, oxygen and other elements that are critical to the function of the biosphere. Understanding relationships between microbial diversity, microbial metabolism and biogeochemistry is one of the great challenges facing microbial ecologists today. Metaproteomics is a new and untried approach to identify proteins present in microbial communities. Proteins are the engines that drive all chemical reactions in cells and can be used to identify specific microbes as each contains unique protein profiles. Thus, identifying proteins in microbial communities will provide information about what microbes are present in a given sample and what they are doing at the time of sampling. This research will apply metaproteomics to marine microbial communities to: 1) compare the protein expression patterns over geographic and temporal scales; 2) identify proteins of particular interest from specific samples; and 3) link specific microbial functions with individual microbial groups. Proteins extracted from microbial community samples will be resolved based on mass and charge to provide an image of the community protein profile. Similarities and differences between different samples will be quantified by comparing these images. Sequence information for specific proteins of interest will be gathered and used to identify both the protein and most probable microbial source of the protein.
This project will provide the first in depth metaproteomic study of a dynamic and highly complex marine microbial assemblage. Metaproteomics is an alternative and complementary approach to metagenomics and environmental transcriptomics. Although many novel microorganisms have been detected in the ocean, the vast majority of marine microbes still cannot be grown in the laboratory. As a culture-independent approach, metaproteomics will address what proteins are actually expressed in microbial communities rather than the potential expression measurements provided by metagenomics and transcriptomics. This project will support two graduate students and provide both with highly interdisciplinary training spanning the fields of microbial diversity, biological oceanography, analytical chemistry, and bioinformatics.
