Using scanning electron microscopy to study microbial communities in speleothem samples collected from Iron Curtain Cave

New microorganisms are continually sought after in the hopes of finding new bioactive compounds, so researchers are looking to extreme environments such as caves to find them. The scanning electron microscope (SEM) can be used to study environmental microorganism colony structure and morphology in a natural state. Sputter coated environmental samples can be used to characterize bacteria, but this method can be expensive and time consuming, making it cost-prohibitive for smaller labs. The aim of this study was to observe and compare cave bacterial isolates on Gold-Palladium (AuPd) coated and uncoated soda straw speleothem samples and from inoculated R2A agar using SEM. The resulting images were then used to describe colony structure and morphology of the isolated organisms and establish which specimen preparation treatment produced the most efficient means of characterization. The study revealed that the uncoated samples generally produced images of similar quality to the coated samples but the image quality was lower at higher magnifications. Although culturing bacteria from the speleothem and viewing them with the SEM proved to be faster than searching the entire speleothem, growth conditions could drastically change colony formation and potentially lead to missed species that are present.