Assessing the environmental activity of ultra-small cells with deuterium oxide labeling and proteomics
EMSL Project ID
50275
Abstract
Reports of ultra-small cell and streamlined genomes have flooded into the field of microbiology, providing support for the idea that the prevalence of streamlined bacteria in nature has been underestimated because they are challenging to culture. The few examples in which cells with these properties have been cultured have revealed them to be well-adapted to growth at low-nutrient extremes, but incapable of rapid growth even after extensive experimentation identified all growth requirements. These observations engendered significant debate about the relationship between growth rate and success. The most prominent example of in this debate is the ultra-abundant and small aquatic bacterium SAR11 (Pelagibacter). The question has arisen, are these cells successful because of superior properties in competition for limiting nutrient resources, or are they successful instead because they avoid predation by viruses and/or grazing organisms? To address this fundamental question, we are developing methods for measuring growth rate of ultra-small microorganisms in the environment by labeling proteins with deuterium oxide (D2O). The results will be used to estimate the contribution of SAR11 populations to global organic carbon oxidation. Similar questions apply to all cells, in all ecosystems, and are particularly relevant to dominant organisms that are adapted to compete in oligotrophic environments, such as aquifers, rivers, lakes, groundwater, and the oceans. In principle, D2O labeling could be applied to measure the relative growth rates of multiple organisms in any growing microbial community. This study leverages the background of SAR11 systems biology, which provides defined growth media, metaproteomic databases, and metabolic pathway knowledge that will support the interpretation of D2O labeling data from cultures and the environment.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2018-10-01
End Date
2021-09-30
Status
Closed
Released Data Link
Team
Principal Investigator