Authored by Grace Pold | April 16th, 2017
People are attracted to life as a scientist for all different reasons. Some join because they want to learn how to save charismatic animals such as birds and bunnies, while others want to come up with new ways to feed the world or develop vaccines to curb the next pandemic. However motivating these questions may be, being a researcher doesn’t always mean living a dream. In fact, with the daily grind of repetitive tasks, worries about funding, and experiments going wrong, perhaps the question shouldn’t be “why be a scientist”, but rather “why stay in science?”
For me, it is the small things that keep me in science. One of my favorite ways to brighten up my day is to do an assay – a measurement of something – in a way that results in a beautiful array of colors. After all, scientists are typically depicted on television surrounded by flasks of bubbling colored liquids, right?
My research looks at how the microbes present in soil may exacerbate the effects of climate change by increasing the rate at which they munch through plant debris and other carbon present in soil. Therefore, most of the colorful assays I do have something to do with measuring the kinds of carbon available to microbes, how they access it, and what they do with it once they have eaten it. All of these things can be measured with a different colorimetric assay. These assays are called colorimetric because we use the amount of a specific color of light transmitted to measure how much of our compound of interest is present. So how does this work?
As has previously been explained, the light we can see exists in a range of colors such that objects appear the color of light they do not absorb. So if a solution has a low concentration of something which absorbs red and blue light, it appears pale green. If that thing absorbing red and blue light is now present at higher concentrations, the solution appears a stronger green color. This rule is called Beer’s Law.
To measure how much carbon there is available to soil microbes, I use a concoction of heat and toxic chemicals so vile it will burn paper on contact. At low levels of carbon, the solution is yellow. At high levels of carbon, the solution is green. If the concentration of sugars is too high for the assay to measure, the solution essentially burns and turns brown. This is like a milder version of the sulfuric acid and sugar experiment you might do in chemistry lab.
After measuring how much carbon is present in soil, I want to know what kinds of enzymes the microbes are using to break it into little pieces they can use. To do this, I can use either colorimetric or fluorimetric enzyme assays. Fluorimetric enzyme assays are slightly different to colorimetric enzyme assays because instead of shining white light through a sample and seeing how much of a wavelength is absorbed, a single colour of light is shone on the sample and we measure how much light of a different colour of light is emitted. This change in colour occurs because some of the energy in the light is held and lost by the molecule which absorbs it. How much energy is lost before the light is re-emitted differs between fluorescent molecules and that determines what colour the emitted light is. So we can shine high energy blue light on something and it might appear red, but we couldn’t shine lower energy red light on something and expect it to emit blue light.
I use colorimetric assays to determine how much microbes break down lignin, the substance that makes wood rigid. I use fluorimetric assays to determine how much these microbes break down cellulose, the part of wood used to make paper.
In addition to measuring all the kinds of carbon in soil, I also have to measure what comes out the other end – the carbon dioxide. Just like humans, many bacteria breathe out CO2 when they are active. I take the gas emitted from the microbes and let it dissolve in a solution, which causes the pH to drop. By measuring how much the pH drops using a pH-sensitive dye, we can determine how much carbon dioxide has been produced.
Actually, there is an abundance of color in my daily lab life even without dyes. Many of the bacteria I – and other microbiologists – work with make their own pigments. These microbial rainbows have been co-opted into a cheer-making friendly “agar art competition”, in which the various shades of bacteria are used as living “paint”. Apparently I’m not the only one who finds a little colorful lab work an effective way to raise their spirits!