Mud, mud, glorious mud!May 14, 2009
I’ve been looking forward to being able to write a “sediment blog” – because it means things are progressing with the sediment experiments!
On Monday, the divers collected 10 large sediment cores for the ocean acidification experiments. These cores have come from the sediment around the pier, which is right in front of the marine lab, and we now have 20 cores which are spread over the 5 pH treatments being used for the other studies. Fred and Pieter will be performing incubations throughout the experiment, to look at the oxygen consumption and nutrient fluxes. This gives us information about the biological processes that are going on within the sediment (such as respiration and growth). Measurements of temperature, total alkalinity, pH and dissolved inorganic carbon will also be taken from the overlying water to monitor the environmental conditions in the cores.
At the end of the experiment, samples will be taken for analysis of nitrification and denitrification. These processes are carried out by bacteria, and are important processes in marine sediment because they allow nutrients to be cycled back into the water column in a form that other organisms can feed on. We’re interested in how ocean acidification might affect this nitrogen cycle in the sediment. Therefore, Karen and I will also be looking at the bacteria that are present in the sediment. We’ll be looking at how the overall diversity of bacteria is affected by ocean acidification, and also whether the genes responsible for nitrogen cycling are affected.
Pieter and I have already taken some sediment samples so that we can have a look at diversity in normal sediment – this will give us a good baseline so that we can tell whether the communities have changed at the end of the experiment. We’ve got two lots of sediment so far: some really smelly, muddy sediment from the pier in front of the marine lab, and some sandy sediment from a site further downstream, called Brandal. As you can see, they are quite different, so it will be interesting to compare the bacteria in there!
So how do we look at the bacteria in the sediment??
Most bacteria cannot be grown in the laboratory, so we have to use molecular methods to look at their internal molecules, such as proteins, DNA, or RNA. To look at diversity (what organisms are there and how many), we look at the differences between the DNA, just as we might look at a human’s DNA to investigate that person’s ancestry. To look at genes which control a specific function, such as nitrogen cycling, we can look at RNA – this is similar to DNA, but it tells us which genes are being made into proteins – so we’re looking at the genes that are actually being used in the environment. We can use “fingerprinting” techniques to look at the structure of a bacterial community, and how it changes.
Extracting DNA – a classroom experiment
You can extract DNA in your classroom from a piece of fruit or vegetable – peas, onions and bananas usually work pretty well. Follow the instructions below … the way in which scientists extract bacterial DNA is slightly different, but it uses the same principles (cell wall disruption, salty environment, protein breakdown and alcohol precipitation) …
Step 1: Dissolve 3 grams of salt in about 100 millilitres of warm water (distilled water is best if you have access to a lab).
Why? The salt provides a “good environment” for the DNA so that it is more likely that the DNA will come out of the cells and into solution (DNA is negatively charged, and salt is positively charged)