In lakes, many things change on daily scales. In this time lapse video of our Windogradksy columns, you can see the water levels rise and fall on a daily cycle as gases are produced and consumed at different times of day. One example is oxygen, which is produced by photosynthesis during the day and consumed at night. There’s also been some cool new research published on how even non-photosynthetic bacteria change on daily scales because of their relationships to the photosynthetic bacteria. (Aylward, Frank O., et al. “Microbial community transcriptional networks are conserved in three domains at ocean basin scales.” Proceedings of the National Academy of Sciences 112.17 (2015): 5443-5448.)
One of the processes we’re interested in the use of actinorhodopsin, a light-powered ion pump. Early this summer, we collected RNA from Lake Mendota at sunrise, noon, sunset, and midnight in order to see how actinorhosopsin levels vary over a day. Last Thursday, we began pursuing this question further by getting higher resolution timepoints. This meant sampling Mendota every 2 hours for 24 hours!
A sampling effort this intense required the help from everyone in the lab. We took shifts throughout the day and night to make this happen. We’re looking at more than just actinorhodopsin with this big experiment. Because it provides a snapshot of what genes are actually expressed, RNA can answer many questions that DNA cannot, such as:
- Are the bacteria we see in DNA samples alive or dead?
- What genes are actually being used by a bacterium at a given time?
- Are there groups of genes that are always expressed together?
- Are these co-expressed genes found across multiple organisms?
- What compounds are bacteria using? What are they producing?
- Does the abundance of a bacterium mean anything about its activity levels?
To answer these questions, we collected DNA, environmental measurements, and samples for nutrient testing along with RNA. Overall, it went amazingly well, largely in part to all of the organization ahead of time by the head of this mission, Pancho!
The sampling started at 6:08AM on Aug 20, and ended 13 samples later at 6:08AM the next day.