Done with sampling!

So after a few months and 400+ samples later, we are finally done with sampling and data collection! The results look good, with several unique key points that we will be looking into once we have sequencing data. It will be interesting to see, and hopefully correlate, the appearance or growth of an organism with a change in one of the chemicals we measured.


On Tuesday I went in to do some DNA purifications to refamiliarize myself with the process and going back to lab overall. Hopefully the purifications and DNA isolation goes well, and we get back some interesting data from the sequencing run.

Back in business

We’ve been sampling every day for Coral Ponds 1 and 2. We are up to almost 500 samples… which means we have a lot of DNA extractions to do.


I’ve noticed a few things in the last month. The coral used to be white, but now it is covered with a reddish algae. This is good because clearly things are changing, which is what this study is about! If macroscopic things (for example, the visible algae) are changing, then the microscopic things (microbial community) are most definitely changing as well!


On a side note, Matt and I discovered the time it took for a full round of sampling at maximum efficiency. With water filtering being the rate limiting step of our sampling process, we focused on wasting no time with the filtering. By this I mean, we had the next liter of water ready to go instantly after the current liter was done filtering. We also set a timer to remind us to keep adding water to the filter. Out of curiosity, I timed our last filtration and it took 17 minutes and 30 seconds. Overall we were able to complete the sampling in about 1 hour and 50 minutes. Being the mathematician that I am (just kidding), I assumed each filtration (6 total) took about 17 minutes and 30 seconds and calculated the time that water was not being filtered from the time we started to the time we finished: 5 minutes! I’d we were pretty productive.

Progress Report

Coral Pond 1 Graphs copy copyThe first coral pond has been running for 49 days now. We have followed them through their initial construction, the inoculation from an established coral tank and now the addition of live rock so that more corals can be added. Our collection of over 400 samples is continuing to grow and we are seeing nice trends in our water chemistry parameters.  We are excited to start looking at the DNA and have been extracting a number of samples.

Here is a quick look at coral pond one. I believe David has already shown some of this data. The red dot is the time point when we inoculated the coral ponds with microbes from an established coral reef tank.

Introduction and my first day of sampling: Undergraduate Aquarium Project

Hello Everyone!

Since I am new to the lab and not many of you know me, I thought of positing a quick introduction along with my first day experiences with sampling.

My name is Lakshmi Bharadwaj, you’ll probably see a lot of me this quarter.


(That is how I look like if you find me walking into the lab, you can say hello!)

I hope that I get to work in the lab with all of you at least once. Here’s a little bit about me:

I am a senior Biomedical Engineering major and I love photography, writing, swimming and microbes! Currently, I am extremely curious about bacteria, and my senior design project is all about how they infect your bloodstream, their clinical relevance and detection. I haven’t really dealt with a lot of microbial procedures: my time in engineering lab has been mostly machine work. So I’m really excited to learn from all of you and also observe how things work in a biology lab!

My first day in the lab was exciting because I hadn’t really seen anything like it before. I got introduced to the basics. I learnt how to correctly obtain the water, sediment and wipe samples. I learnt of the rate-limiting step in the procedure, proper techniques etc. Then, David taught me some lab protocols that I needed to follow. I was really glad with the pipettes that the lab uses because I find it extremely convenient. The only one time I have used micropipettes before involved stops and was slightly confusing. I find our pipettes so much easier to use.

I also got a basic understanding of what water chemistry involved. I learnt about how there were different tests for different chemicals and all of them required a different procedure. Although I couldn’t perform all the procedures, I got a pH reading and observed how oxygen levels were tested for.  I hope to perform each test individually and learn it in greater detail next time.

I was half-way through testing, but I had to abandon it last minute because of incorrect dilution. I did obtain a fair understanding of how this should be done in my two and a half hours in the laboratory though.

During my time in the lab and with the genome project, I hope to use this blogging space to document my observations and have it act as my notes/log book. You should expect a blogpost from me weekly.

I wish to come in every week, probably on Tuesdays or Wednesday mornings and I look forward to meeting everybody.


Water Chemistry 10 Commandments

So for this aquarium project we have been doing a ton of water chemistry (over 50 hours so far).  Along the way we’ve learned a number of lessons the hard way and so have written up a set of “Water Chemistry 10 Commandments”.  I’m posting them here for both the current students or for anyone else doing water chemistry analysis.

1. Wear gloves! (seriously… reagents include mercury, corrosives, and carcinogens)

2. Double-check all reagents!!! For example “sulfuric acid” ≠ “sulfamic acid”.  Likewise “phosphorus” ≠ “phosphate”.

3. Be sure your measurement is within the range of the test.

4. Be sure to keep track of “ppm” versus “ppb”!

5. Replace the cap of each solution immediately! Spills are expensive, hazardous, and annoying.

6. Rinse all glassware with the sample to be measured before conducting an assay

7. Always rinse everything between measurements and assays.   The pH meter should be rinsed in tapwater, everything else should be rinsed in DI water.

8. Dilutions should be performed with DI water.  Be sure to measure the concentration of whatever you’re testing in the DI water first so that you can subtract the background.  The blank needs to be of the diluted solution as well!

9. Keep cuvettes clean!  Clean before each use… wipe with a Kimwipe immediately before placing in detector.

10. If you get an anomalous measurement: do it again twice more.  Sometimes things really do change but if you’ve been getting ammonia measurements between .5ppm and 1ppm for days and then all of a sudden you see 25ppm… it’s worth making absolutely sure!

Preliminary Nitrite/Nitrate data just for fun

Since we’ve been collecting all this water chemistry data I thought it’d be nice to share a bit of it.   Here you can see the nitrate and nitrate levels in Coral Pond #1 over a couple of weeks.  Levels start out low, then rise in the newly established system right up until inoculation with an stable microbial community.  At that point the nitrites head back down quickly and the nitrates continue to rise.  So question for the undergrads on the project:  Is this what we expect or not?   Why would we see this pattern?


A tale of two stoppers (one of which is a rip-off)

For the water filtration we’ve been using Supor PES membrane filters (.1um), supported using a fancy filter holder from Millipore. (both recommended by Laura Sauder from the University of Waterloo).  So far this setup has worked pretty well, although obviously a bit slow when there’s a lot of sediment in the water.   However, last night the rubber stopper that holds the thing together cracked and got sucked into the vacuum flask.  Which is pretty much a one-way trip… It’ll probably stay there forever.   So I looked at the Millipore website and they want $100 + shipping for a replacement stopper!   It’s a piece of rubber (well silicone actually) with a hole in it.  Sheesh.

So after consulting with Russell in our lab, he directed me to Central Services on campus where I bought a rubber stopper for $1.05 and they drilled the hole for free.   As a bonus, it actually fits better and is easier to use than the one that costs one hundred times as much from Millipore.

Sampling yesterday

Yesterday we did PM samples on both Coral Ponds after they were inoculated. Our rate limited step (the water filtrations) took even longer because there was so much sand in the water. The sand would collect on the filter, causing the water to pass through much slower. We didn’t filter the water from Coral Pond #2 because there was so much sand that I think the water filtrations would have been unsuccessful. We did take water samples and left them overnight so that the sand would settle and David filtered the water this morning. We did run all water chemistry tests on both Coral Ponds last night.

Because our nitrite meter only measures up to 200 ppm, I did a 1:4 dilution for the water from Coral Pond #1 and a 1:10 dilution for the water from Coral Pond #2 in order to get readings within the range. Then I multiplied to get the correct value.

New beginnings for old tank as new coral ponds

The last two days have been busy for our coral ponds and the microbial communities adapting to the new habitats.

Yesterday we put the sand and seawater into the second coral pond. We collected samples from the sand and water before and after mixing. The freshly set up pond was and remained relatively turbid overnight as a result of fine particles from the sand.


We also noted that the first coral pond had a protein skimmer installed to help keep the water clean. David noticed that with the addition of the protein skimmer there was a rise in the pH. You can check it out yourself using the tweetameter. This morning we did a full chemical analysis and microbial sampling on coral pond one to catch any changes that might be happening in the microbial community as a result of additional filtering.


Today was the big inoculation day as one of the established coral tanks was torn down and placed into the two new coral ponds. This included the rocks, numerous soft corals some snails and hermit crabs along with all the sediment from the bottom of the tank. Unfortunately adding the old sand (while important to establishing a healthy microbial community into a new aquarium system) had a terrible impact on the clarity of the water. Due to the probable negative impact the high sediment load would have on our water chemistry kits, sampling was put off until an afternoon sampling.

Dismantling the Coral Tank


Pond 1


Pond 2


Hopefully the water has cleared and good luck to those of you doing the afternoon sampling. I will be checking in on the ponds again in the morning.