It was a beautiful day at McMurdo today, one of the warmest we’ve had yet. It would have been a spectacular day to be out in the field but unfortunately we had a lot of lab work to catch up on. On Monday we collected a total of 14 sea ice cores from two different locations in McMurdo Sound. 12 of these cores we sectioned into top, middle, and bottom and set them aside to melt. When these finally finish melting (just checked them, they still have a ways to go) we will pump the melt water through filters that will collect all of the ice algae and bacteria from the water. Back in Seattle we will extract RNA and DNA from the bacteria and conduct our analysis.
Shelly, lost in a universe of little blue dots. Counting bacteria can be an art. Two people will count the same slide and come up with slightly different numbers. To make it easier to compare between samples and studies it is best to have one person always conduct the counts. In the Deming lab this task usually falls to Shelly, and we are grateful!
The remaining two ice cores, one from each station, we call “physical cores”. From these cores we collect biological and physical data that helps us understand the environment that the microorganisms are living in. This data includes the salinity and temperature of the ice, the amount of chlorophyll present (an important indicator of how much photosynthesis is going on), and the number of bacterial cells present. To get this information we use an electrical saw in a room kept at -1 C (30 F) to cut the cores into 13 cm and 2 cm chunks (watch the fingers!). The 2 cm chunks get melted straight away and from these we measure salinity. The 13 cm chunks get melted (like the larger core sections for DNA and RNA) into that sterile brine that we’ve been making over the last week. Fractions of this get filtered for chlorophyll, cell counts, and the other analyses that we’d like to perform.
Epifluorescent micrograph of a sea ice sample at 1000x magnification. The small blue dots are bacteria, the orange is organic debris. The thin blue line is a pennate diatom.
Our whole project is focused on bacteria, so the one thing that we really want to know at this point is how many bacteria are present within our samples? To figure that out we need to take a look under a microscope, which is how Shelly spent a good part of her day. Bacteria are very small, one millionth of a meter or smaller, so not just any old microscope will do. In microbiology we most often use a special type of scope called an epifluorescent microscope. Epi means the light is being projected on the slide from above, not through it from below. Fluorescent means that the bacterial cells are being induced to give off light, or fluoresce, which makes them easier to see. To do this you have to stain the cells with a dye. The dye binds to DNA, and if you shine an ultraviolet light on DNA bound with the stain it will give off blue light. This doesn’t let you see many details of the cells, for that you need an electron microscope, but it allows you to count them and see some general characteristics.
Epifluorescent micrograph at 1000x for a seawater sample.
The top photo is from sea ice. The small regular blue dots are bacteria while the orange is organic debris. The faint blue line in the lower right quadrant is a pennate diatom, one of the two morphological flavors of diatoms. The other type of diatom is the centric or circular diatoms. Most sea ice associated diatoms are pennate diatoms, so this one seems to be in the right place…
The bottom photo is from water below the sea ice. Notice how regular the cells look and how little debris there is! The bacteria in the two photos are probably dramatically different, but there is no way to know this looking at them under the microscope. It will be many months, after extracting the DNA, sequencing it, and processing the data that we know any more about them!
