Hi everyone! So today was our third official day actually in lab, and at this point our project is well underway. To try to identify the different kinds of bacteria present on our bamboo leaf sample, we’re using both culture-dependent and culture-independent techniques. Culture-dependent, as the name implies, means that we’re trying to culture our bacteria samples on agar plates—we’re trying to grow (hopefully pure!) colonies. We’ll then use various techniques, such as staining, to try to identify our bacteria. At the same time, we’ll be performing culture-independent techniques to try to identify microorganisms on a genetic level. By extracting and amplifying a specific sequence of DNA from bacteria, we can compare their different genetic markers to determine the phyllosphere of our leaves. For our first journal club (next Monday!) we were assigned to read an article from the Journal of Applied Microbiology, Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere (E. Yashiro, R.N. Spear and P.S. McManus. (2011) Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere. Journal of Applied Microbiology 110, 1284-1296). The article discusses both culture-dependent and independent methods of examining the bacterial community of apple leaves, using techniques similar to what we’re doing in lab, and mentions the fact that they were one of the first groups to directly compare the effectiveness of the two techniques (culture-independent produced more data on a wider range of previously unknown bacteria). Since this article was only published a year ago, it’s exciting that we get to follow in their footsteps and be one of the first groups to compare both techniques on a previously undocumented community of plants—who knows, maybe we’ll discover a new species of bacteria!
Today in lab we worked on both culture-dependent and independent techniques. The bacteria we plated last week grew into hundreds of gorgeous colonies (see pictures) of all different colors! We had bright yellow, dark orange and neon pink colonies! Our task for the day was to spread individual colonies onto new agar plates so that we can grow pure colonies of distinct bacterial strains. Before spreading, we began working on the culture-independent portion of our project, which involved extracting DNA from the bacteria on plant leaves using an intricate protocol of vortexing and centrifuging. Overnight, specific sequences will be amplified using PCR, and on Friday we’ll get to run the samples on a gel and find out if we’ve done everything right so far, so I’ll keep you updated on how that goes! For now, enjoy pictures of our rainbow bacteria!