by Ed Tripp, University of Nottingham
Not all goes as planned.
As I discussed in my last post, by June I had started to collect lichen samples in order to investigate their recovery in heathlands. This process is simple. You go to a heathland site with some pots, scissors and gloves. After eventually finding a patch of lichen, you carefully cut off a small sample and put it in a pot to take back to the lab.
Once the samples have been collected, I needed to isolate the fungal part of the lichen, grow it on an agar Petri dish, and then do DNA analyses on the resulting culture. Lichens are symbiotic organisms, made up of fungal and algal partners. If I was to try to get DNA from raw lichens, I would get a jumble of fungal and algal DNA. This is why I needed to isolate just the fungal partner from the lichen.
This is where numerous problems began. To isolate the fungus, I ground the lichen up in water, and then, using a microscope, I picked out fragments that appeared to have no algae cells. I then placed the fragments on agar.
Problem 1: The agar is designed to be a perfect place in which to grow fungus. This is fine when growing the fungus that I want, but not if other fungus spores get onto the agar. Unfortunately, lichens are covered with fungal spores. These grew very quickly once the fragements were on agar. Each time a fragment was contaminated with an invading fungus, I had to throw it away.
Problem 2: Algal cells are tiny. It takes just one cell on a lichen fragment in order for the algae to grow. After a couple of months, I could see green algae beginning to grow on some of my fragments. Therefore I looked at some of my "algae-free" fragments under a very high powered microscope. It soon became clear that most of my "algae-free" samples were not actually algae-free at all. Again, any contaminated fragments had to be thrown away.
It takes a long time to work on each lichen sample, so it took me just over three months to complete the work on all my samples. By this point the problems with algae and fungus contamination had caused me to loose a significant number of my samples. After spending time to investigate ways to counteract these problems, which were not successful, by October I had becided that it was best to cut my losses and give-up.
I hate giving-up, and do my best to make sure that I never have to give up on something. But sometimes science doesn't work. With the best of intentions, and all the time in the world, if something just cant be done then you just have to move onto something else.
I hope to come back to my lichen samples in the future. I have a number of different methods that I would like to try...I will just have to hope that these are more successful!
Next time I will talk about what I decided to do for the next chapter of my research.
Below are a couple of pictures of fragments that had been infected with algae and fungi.