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Color
Coloration is one of the most noticeable differences in colonies on distinct agars and is caused by the difference in nutrients in each agar. For example, a colony of Salmonella bacteria on general agar like R2A appears a neutral color and is similar to colonies of other bacteria and yeasts on the same plate. After an analyst takes an isolated colony of the Salmonella and places it onto a selective agar like xylose lysine desoxycholate (XLD) agar, the cells grow into a red colony with a black center. This new color appearance results from the Salmonella producing color after metabolism of the new nutrients present in the XLD that were not there in the R2A.
Size
Each colony of microbes on agar medium is the result of the multiplication of one or more microbial cells present at that spot. The rate at which the colony spreads and therefore appears bigger depends on the characteristics of the medium. For example, Aspergillus niger mold will spread quicker and therefore each colony will be larger on specialist agar such as Sabouraud Agar (SDA), which contains optimum nutrition for the mold, than on nonspecialist media such as R2A. The agar content of a medium can also affect the rate at which a colony grows, as cells that are motile (can propel themselves around) can spread further in media with low agar levels than media with thicker agar.
Shape
The shape of a colony can also vary with each medium. For example, yeast in a sample that is not placed on top of the medium but is mixed in with a pour plate technique can grow jaggedly instead of in a circular fashion under the top of the agar, whereas the colonies on the surface grow flatter and in a round shape, which is due to the oxygen availability and the freedom of movement through the agar.
Agar Alteration
Certain agars contain a special ingredient which a species of microbe can break down. An example of one of these agars is blood agar, which contains some animal blood. Species such as Streptococcus pneumoniae, a human pathogen, can break down blood. This means that a colony of this species on blood agar will produce a green coloration on the agar which would not be present on agar without blood. Microbes that are resistant to a particular antibiotic will also produce a clear zone around them, only on agar which contains the antibiotic.
Development
Sometimes a species in a colony will have unusual characteristics on the cells themselves due to the type of agar they grow on. One such example is Salmonella enterica typhimurium, which can live as cells without a flagella (a propeller-like feature which allows the cell to move around) or as cells with flagellae, depending on the media. Certain carbohydrates are necessary building blocks for flagellar structure, and the absence of these nutrients can prevent the cells growing flagellae.