Closed NatalieDreux closed 5 months ago
Providing information on the metabolomic aspect of the project. i.e. How much water per samples (5mL), storage, etc.
Reached out to Liz for clarification on metabolite mixes
Subsequent question: how much will sampling throughout add to the project cost?
What is the expected timeline for the incubation? Are we shooting for 24 hours or 48 hours?*
Are we going to want biological replicates or technical replicates
Water samples provided from Liz, sampling from surface level. We are electing to use whole water and not filter our larger organisms Usure of sample quantity/size
Genomics: Samples should be ~500mL filtered down onto Mill Metabolomics: Samples should be at least 5mL, meaning ~15-20mL per time point accounting for triplicates and excess:
if technical replicates the sample would be aliquoted into 3 separate 5mL samples (similar to the Pro11 MIT experiment). If biological replicates, 5mL samples from each ‘community’ [ i.e. each incubation (control, Pro, Micro.) ]
Incubation period of 24(?)hrs with timepoints of T0,Tx,Ty,T24
Could do T0, T6, T12, T24 T0, T12, T18, T24 T0, T8, T16, T24
- Max: i think that we should focus more on the front end of the incubation period rather than the end
24: 0, 6, 12, 24
36 0, 12, 24, 36
48 0, 12, 24, 48
- (only reason i wouldn’t go further than 12hrs for the second point given the large time frame is because I really do think the front end of the experiment is the most important but given a time frame like 48 hrs i think getting points 12 and 24 would allow for a relatively early timepoint (12) that would provide initial(ish) uptakes of the metabolites and then 24 and 48 would allow for a decent enough time for divisions to take place for community structure change to occur. Same line of thinking applies to the reasoning behind the 36 hour points.
Are metabolites and genomics being measured at each of these timepoints or is it just metabolites and genomics only at T0 and TFinal?
More so thinking about the genomics
We ideally will have a control and two other sets for our two organisms metabolite mixes. If we did two treatment groups and a control, 4 timepoints, and duplicates, this would likely use all 24L of our water allotment.
Example: at T0 samples would be taken as follows ~
- Control A
- Control B
- Treatment 1A
- Treatment 1B
- Treatment 2A
- Treatment 2B
Using metabolite mix from Prochlorococcus and Micromonas
So the implication being that whatever is growing and consuming the metabolites during the incubation period are favorable towards the excretions of the organisms we took the metabolite mix from. This could reveal some interesting dynamics between the phytoplankton and microbes present if there are differential observations between samples.
Genomic investigation to be done in Dyhrman Lab
This is most likely happen at WHOI as sending samples with chemicals is a hassle from Bermuda and there will likely be no time to do the PPL SPE needed for analysis to have ‘dry’ samples to send back
ID will also be at WHOI using LC-MS, Skyline, etc.
Me and the B2P 23 cohort will be designing a incubation experiment, taking place in Bermuda, as part of the C-CoMP program. The main task for now is to come up with a rough draft of how we want to preform this experiment. Taking into consideration things such as: the water budget, what measurements we are taking, sample types (bio/tech), etc. This will be a deliverable for the 3/8/24 B2P weekly meeting with Vicki, where Liz will be in attendance to answer some questions.