It's not a stretch to think some bacteria might modify this internal environment to better suit their own needs. Could some bacteria influence plant metabolism to take care of their host, so the colonizers have a safe place to live? Alternatively, maybe some other bacteria weaken their host to make it easier to consume them? Even more fascinating is the possibility that some bacteria might attract herbivores to feed on their host and in the process help spread the infection to other plants? It's conceivable there are many types of interactions between the microscopic and macroscopic communities.
To understand these putative interactions, we first need to identify the types of bacteria that live inside of plants. To do this we collected leaves from a variety of plant species living in Gothic, CO. Since we are interested in the internally living bacteria, we first had to sterilize the external parts of the leaves. We washed each leaf in a series of water, ethanol, and bleach to clean off any bacteria living on the surface. We stored these leaves in the freezer at -80 degrees Celsius. This kills the cells but preserves their genetic material.
The genetic material in the leaves will be analyzed to identify the types of bacterial cells living inside. Genetic sequencing is useful because it samples all cells present in the tissue. Traditional methods of cataloging microbiome communities involved growing bacteria on agar plates. However, the limitation of this method is that only bacteria that are able to grow on agar will be identified. Many types of bacteria simply won't grow outside their normal host. By cataloging all the genetic material present in the tissue, all the bacteria can be accounted for whether or not it can be grown in the lab. The sequencing information can sort out plant cells from bacteria cells and assign an identification to all the bacterial species found.