Counting archea/bacteria in SEM images
The image below shows a cross-sectional view of the Deep Mine Microbial Observatory (DeMMO). Situated in the former Homestake gold mine in the Black Hills region of South Dakota, USA, DeMMO is a network of legacy boreholes that intersect fluid-filled fractures spanning depths of 800-4,850 feet. The grey lines are tunnels and shafts in the mine, and the green dots are the locations of boreholes drilled into the tunnel walls. The boreholes marked by the large dots are called DeMMO1, DeMMO3, and DeMMO6.
Watch this short clip to see how we installed flow-through bioreactors in the outflow of the boreholes at DeMMO. The bioreactors were filled with minerals representative of the host rock lithology or inert glass, and over time these materials were colonized by bacteria and archaea. Inside each bioreactor, we included a polished chip of mineral (pyrite, hematite, siderite, magnetite, pyrolusite, calcite) or a glass slide - these were imaged using a scanning electron microscope (SEM).
The image above shows a polished chip of the mineral pyrolusite (MnO2) that was included in a bioreactor and an SEM image we took of the pyrolusite surface. Microbes are highlighted in green.
For each mineral type used in the bioreactors, we took ~20 photos. We need to count the number of cells in each photo in order to calculate cell densities on each mineral type. Ultimately we want to know which mineral the microbes liked best!