Join the Microverse Project for schools and nature groups: reveal invisible urban ecosystems!

Anne D Jungblut — Sat, 27 Dec 2014 17:58:08 GMT

Today I would like to write about a very exciting new and free science project for upper school and nature groups all around the UK called The Microverse.

You may not have thought about what a microbe is before, but there are millions - possibly billions - of different kinds. So why should we care? Well, firstly, most life on earth exists because of one group - the cyanobacteria. Then there are all those important ecosystem services that microbes provide. And remember the 'healthy bacteria' in your gut, which have been linked to all sorts of health benefits (or diseases, when things go wrong).

We now know that human activity is changing the world we see, but what is it doing to the world we can’t? Nobody really knows. There are many questions to answer about about the microbial diversity that can be found in urban environments in cities, towns and villages. What is microbial diversity like on concrete pavements and glass skyscrapers? How can they survive the temperature extremes, lack of nutrients and high levels of pollutants?

The Microverse project is asking schools and nature groups to take samples from buildings for analysis at the Natural History Museum in London. Are our cities a disaster for microbial diversity, or are there thriving, species-rich communities out there? Who knows? It’s a whole new world we’re entering. More information on the biology, science and activities in this Microverse clip.

It is is easy and free to join the project. Just sign up on the The Microverse webpage.

Summer Antarctic cyanobacteria adventures: problems with PCR

Anne D Jungblut — Mon, 20 Oct 2014 16:38:09 GMT

Summer student Josi has been working with Dr Anne Jungblut on the Museum's cyanobacteria collections. Her next post on cyanobacterial diversity is all about DNA lab work.

At the end of my last post, we determined which cyanobacteria isolates were unialgal by microscopy and suitable for DNA analysis. These samples were initially collected during the Antarctic fieldwork featured on this blog, stored, and brought back to the Museum. Now we want to know what type of cyanobacteria we’re dealing with! One method to determine the species is by DNA sequencing. For cyanobacteria it is really important to use DNA analysis, as cyanobacteria have very varible morphologies that can change under under different growth conditions.

Analysing DNA

The first step of preparing the samples is to carry out a DNA extraction. This step destroys the cell wall of cyanobacterial cells, and removes everything but the DNA from the test tube. A cyanobacterial genome is fairly large, around 1-10 megabases. That’s as much information as fits on a CD-ROM! Therefore we want to look only at a smaller section of DNA at this stage. The step after DNA extraction is called a PCR (polymerase chain reaction), which amplifies a small part of the DNA and generates multiple copies of it. We are using a cyanobacteria-specific protocol that only targets the DNA of cyanobacteria.

Sounds straightforwards, right? Well, this summer I was the victim of the PCR ghoul - none of the reactions worked...or rather, they worked too well. Below you can see the results of one of my (many…) failed PCRs. Each white stripe corresponds to the amplified DNA after PCR of each sample. The 'ladders' on each side are the equivalent of rulers to allow you to verify the size of your amplified DNA. Looks pretty good, right? We’ve got a good yield for each reaction!

Wrong - unfortunately, the white stripe on the far right is a negative control. I set up the PCR for that reaction without any DNA, so actually, there shouldn’t be any stripe showing up at all! So what’s going wrong here?

PCR results from Cyanobacteria (16S rRNA gene) isolated from Antarctica and contamination in negative control.

Well, the PCR amplifies only cyanobacteria DNA - so there can be only one explanation for the 'positive' negative control. One of the reagents for the PCR has DNA contamination! The only solution to this is trial-and-error elimination - each reagent must be replaced individually to figure out the culprit. Unfortunately, a PCR reaction requires about 8 different reagents to work, and any one of them could contain a tiny trace amount of cyanobacterial DNA.

You can imagine that this process takes time, and can at times be disheartening, especially as the contaminants cannot be seen with the naked eye. However, luckily, the PCR ghoul finally released me from my odyssey and my negative control was finally 'negative' without a white strip, and I was able to send my samples for DNA sequencing. More on the results next time!

PCR results from Cyanobacteria (16S rRNA gene) isolated from Antarctica without contamination.

Blog Posts From Exploring cyanobacterial diversity in Antarctica Blog Tagged With sequencing

Join the Microverse Project for schools and nature groups: reveal invisible urban ecosystems!

Summer Antarctic cyanobacteria adventures: problems with PCR