Day 1 of Coral Pond #2

Today they established the second Coral Pond (Coral Pond #2 for naming purposes). They are going to innoculate both tomorrow.


We came in at 10 this morning to do some water chemistry on the incoming water for Coral Pond #2. Then we took samples and are currently doing water chemistry for time 0 of Coral Pond #2. However, we took water from Coral Pond #2 right after they loaded the water onto the sand, so the water was turbid, resulting in some questionable data. For example, nitrite and nitrate readings came out as zero. I think this is due to the turbid water, so we are going to do the test again on the filtered water. We’re just waiting on the filtering water… 3 x 1 Liter takes about 1 1/2 hours – Definitely the rate limiting step.


We’re doing AM and PM samples for the next three days.


In other news we’ve reached triple digits for # of samples 🙂

Gonna be a busy week!

And I don’t mean with Finals! (just kidding, finals included!)


But in terms of our project, they are putting water into the second coral pond on Tuesday. Then they are going to inoculate both ponds on Wednesday with the tropical reef tank sediment. At this stage it is extremely crucial that we sample frequently because microbial communities will be rapidly changing. We’ll be doing AM and PM samples all week during our study breaks. On Monday we will sample the tropical reef tank before they transfer the sediment into the coral ponds. We will also sample the incoming water for Coral Pond #2.


When Friday comes around, we will run into another problem. Us undergrads are going home for three weeks, which leaves David and Matt a lot of sampling and water chemistry. Fortunately, sampling only takes a few minutes and can be stored in the freezer until we all get back. Water chemistry takes a bit of time, but with the new water filters on their way the process should be quicker than it has been.


And when we get back we’ll only have a couple hundred DNA extractions to do… no big deal. But for now, we’ll focus on this week. Sampling + Studying! Anyone want to quiz me while I measure nitrite levels in the water?

Continuing with the sampling and water chemistry of the new coral pond

They’re going to add old sand, rocks, and animals from old reef tank next week, which will be crucial in our succession study. Fortunately (not!) next week is finals week for us undergrads. So basically our study breaks will consist of Sampling and water chemistry! 😛


Then over break David and Matt will get to have all the fun while the rest of us go home. But when we come back there will be so many DNA extractions to do I won’t even know where to start.


Today I did some DNA extractions from Day 1 and 2’s sediment samples of the new Coral Pond.

Can’t think of a better way to spend my Saturday afternoon!

Unlike most Saturdays, today I woke up and my first thought was, “I get to go to the SciLab building and sample!”  Jennifer and I took samples of the wall, water, and sand in the Coral Pond. We also did all of our water chemistry tests. Everything went well!


My only concern is with the nitrite test that I did. My value was extremely higher than the first two times (before the water was added to the pond and time zero). Those values were around 20 while I measured nitrite at 125 today. Because of this significant difference I ran the test twice, but got the exact same number the second time. I’ve been trying to find anything online that would give me a hint to whether my value makes sense or not.


We are going to have a lot to do this week. DNA extractions here we come!

Day 1 of sampling tomorrow! #OccupyBioLab

We have received word that they’re loading the first container with water tomorrow, which means we will have sampling and testing to do! They’re graciously lettings us keep our water chemistry equipment in the labs so we don’t have to bring it back and forth from the Genome Center. Also they’re giving us some freezer space. How nice! 🙂

Water Chemistry

So I meant to post this yesterday, but I couldn’t figure out why it wouldn’t let me blog. Apparently my computer signs me off wordpress every so often so I have to sign back in.. So this information is from my time in the lab yesterday.

Dissolved oxygen, nitrate, and ammonia tests came with no reagents… really? It’s almost as if they expect us to have an abundance of reagents for nitrate test before we have the tools to run the test. Oops, our bad! So that’s a bit frustrating, but we ordered more reagents for everything which should come by tomorrow hopefully.


The Phosphorous and Nitrite kits came with a couple reagents (still annoying), but this allowed us to run a couple trial runs with them on salt water from one of the tanks. Alex did a few tests in the morning (check out her blog entry) and I did a few in the afternoon.
I’m glad I familiarized myself with the tests because I had to make a few modifications to the procedure, because it was just… not good. For example in these tests, you have to blank the meter (makes sense, right?) but then you have to add the reagents from a small packet into a small cuvette (harder than it sounds) and mix for at least two minutes according to the instructions. However, the meter turns off after two minutes. I solved this by having two cuvettes: one to blank the meter and one with the reagent in it.


Phosphorous gave a reading of 200 ppb, which leads me into our next problem. The meter maxes out at 200, so we can assume phosphorous is at a level higher than 200. We need to get another kit with a meter that measures a higher concentration of phosphorous. I measured Nitrite at 70 ppb, which was similar to what Alex measured.


I also measured pH at 7.46 and salinity at 48.3 mS


David and I hoped that the hardness and alkalinity tests would give similar results since they both test for CaCO3. If we had gotten the same result, we could eliminate one of the tests and save time. I measured alkalinity at 114ppm CaCO3. When I ran the hardness test, it didn’t work. I attempted twice and had the same result: failure. We’re thinking the test just doesn’t work with salt water? We’re going to look into it.


It was really good to familiarize myself with all the equipment because now when we begin our intensive sampling and testing of the succession of the coral ponds, I’ll be ready to go with those water chemistry tests!


And now we wait! We wait for an email telling us they’re going to load the water into the containers for the coral ponds. At this point we have a lot of sampling to do! I’ve decided to call it Occupy Bio Labs since we’ll be spending quite a bit of time in there 🙂

Another note on sampling

After discussions on sampling methods, we have decided on new samplings methods. Since we are getting rid of all 18 current samples, our new sampling methods will hopefully be consistent through out the whole project.


For the water samples, we will take 3 x 1.5 Liters of water in one Coral pond.


For the sediment samples, we want to take less than we have in the past. We plan to use 2 mL centrifuge tubes and fill them to the 1 mL mark. We will make sure to get a mix of oxic and anoxic layers of sediment.


For the wall scrapings, we will use a Kim wipe to vertically scrape up and down in one location on the inside of the container. We will put a piece of tape on the top of the container where we sampled, so we don’t sample there again (because there won’t be anything there after we scrape it off). This is important because we will be doing a substantial amount of sampling for our study on succession of the Coral ponds.


On a side note, we are also discussing whether we should sample from both coral ponds or just one. (They are identical in terms of maintenance and what is put into them) We haven’t come to a decision yet.

Thoughts on water chemistry kits and our current samples

Now that we have some of our new water chemistry equipment, we have discussed flaws in our first 18 samples. We collected all 18 samples with no tools to collect metadata (water chemistry). We have decided to take all the samples again and get rid of the 18 we already have. We still don’t have all the water chemistry equipment we need, but it should all be here tomorrow. It is crucial to determine the water chemistry at the time of every sampling. (During our study of succession on the coral ponds, this will be a lot of water chemistry testing!)

Schedule for the new Coral ponds!

We have received a tentative schedule for the new ponds that we will be studying succession on.

Right now they (the people who set up and monitor the tanks) are rinsing the containers with freshwater as well as rinsing the sand with freshwater. The sand is going into the containers as they are getting rinsed. We will take a few samples here before anything else gets added.

Then they will fill the containers with new saltwater and run pumps for a few days with just the new seawater and sand. (too make sure everything is working well) This should be done by mid December. We will also take a few samples here.

Still in mid December (hopefully) they will  add old sand, rocks and animals from old reef tank.  This is where we will start extensively taking samples because we really want to see how the microbial communities become established. We will sample lots for the first couple days and slowly decrease the amount of sampling for the following few weeks. This is because we know most of the changes will happen within the first couple of days.
Then they are going to add live rock that have been curing. Curing basically gets rid of the dead stuff so the live and healthy organisms can thrive! We will again sample more extensively immediately after the rocks are added to catch the rapid changes happening to the microbial communities. We also might sample the rocks before they are put into the ponds.
After a short adjustment period due to all the new organisms, they will begin to populate the ponds with corals and other inverts. Once again we plan to sample a lot for the first few days but continue to sample, but less often after the first few days.

The next change that we predict will occur when students begin to reach into the ponds in the Spring. We will sample during this time too, to see how human interaction affects the microbial communities.


That’s the plan for now! 🙂

Gotta love those DNA extractions :)

Because I was so late to introduce myself, I can also talk about what we’ve been doing for the last few weeks. We’ve gone to the aquariums and collected samples, done some DNA extractions, and done PCR on our samples. Our samples came from salt water and fresh water tanks and include water, sediment, and gunk from the walls of the tanks. Our latest issue has come after PCR, while running the Gel. It seems like our issue might be all the way back in PCR A. I am very excited for the new aquatic systems that we will start sampling in the next couple weeks. We are hoping to start sampling the minute they load the tubs. Our hope is to sample very frequently in the first couple days because we know much of the microbial community will develop in this time. So what’s the point of that, you ask? Well we would love to study the succession of microbial communities in these new aquatic systems.  That’s all for now!