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!

New Coral Ponds

Hi all,

I have been looking forward to adding some blog posts on this great student outreach project but keep holding back because I wanted to include some pictures. I have recently joined Eisen’s lab and will be at Davis for the year before returning to San Diego State University to continue working on my Phd looking at microbial communities across Southern California kelp forests. I was excited about the opportunity to join in on this project and am impressed by the level of student participation.

This week has been busy with everyone getting acquainted with all the new water chemistry kits David has ordered for us. With Russell’s new tweeting pH meter, I was afraid the machines were taking over but it turns out undergrads and grads are still needed for bench work.


Today we got to see the newest coral pond setup and everyone in action as we collect our baseline data. Despite the rain we had a lot of participation and everything went smoothly.


Follow the pH meter on Twitter

As part of the environmental monitoring of the coral ponds that we’re going to undertake Russell has agreed to loan us his famous tweeting pH meter.   Right now it’s just practicing in a freshwater tank at the facility but soon it will go into the first coral pond and we’ll get a continuous record of pH over the course of the project.   Follow along on Twitter @RussellspHMeter


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 🙂

Water Chemistry!

Most of our new gadgets and gizmos for water chemistry have finally come in, so we have started testing them out. Some of the kits we ordered include tests for nitrate, nitrite, phosphorus, chlorine, hardness, sulfate, and iron. At first, we were testing the kits out on tap water to get comfortable with all the tests, and then Matt collected sea water samples from one of the tanks so we started using those.

Today I tried the nitrate kit, which has never been used before. It was a surprisingly simple and quick test, and I found 79.5 ppm (mg/L) nitrate in the sea water. Unfortunately, I do not know the significance of this value, so David suggested that I try the test on tap water for comparison. The amount of nitrate in the tap water sample was 23.2 ppm (mg/L). According to Wikipedia, marine aquariums are only supposed to have trace amounts of nitrate in order to be healthy, so I do not know what our values mean.

A few of the kits we ordered do not have the range to collect values from sea water, so we are thinking of diluting our sea water samples with DI water. We will then use that mixture to conduct the tests that did not work (i.e. the phosphorus and hardness tests). In order for this plan to work, however, there must be small amounts of chemicals in the DI water or our data will be skewed. I checked the level of phosphorus in the DI water and the value came out to be 34 ppb. I am not sure if this means that our dilutions will work, but I am sure we will be able to figure out how to analyze our data after doing some more research.

Water Chemistry Testing Acclimation

The water chemistry kits seem to be pretty straightforward, with a few nuances here and there. I conducted the titration-based tests as well as the tests to detect phosphorous and hardness. For the tests I used DI water to compare values, and so far the values I have been getting are comparable to values other people are getting, as well as make sense, which is good. 

So a few tips. The phosphorous meter turns off after a few minutes, and it will forget the blank sample. So it is a good idea to make the reagent+sample tube before you begin. 

Also, it is good to choose the low range of testings, because the high range is too much for our samples.