How many atoms has the smallest known bacterium?
Let's take the example of the model bacterium E. coli, for which one can find the numbers for a wet cell of a dry mass of 0.28pg. If you have a feeling for how much smaller the smallest known bacterium is compared to E. coli, you can ballpark things.


The number of carbon atoms in a single E. coli cell is approx. 7x10^9 carbon atoms. 
The ratio of elements in E. coli is C : H(1.77) : O(0.49) : N(0.24) .


More simply, if you multiply the ratios by 4, you get the ratios of approximately 4 carbons, 7 hydrogen, and 2 oxygen atoms for each nitrogen atom.

Taken together, there are approximately the following number of atoms in an E. coli cell:

C: 7 x 10^9

H: 1.23 x 10^10

O: 3.5 x 10^9

N: 1.75 x 10^9

That is around 2.4 x 10^10 individual atoms. As you may have noticed, these numbers do not have any bearing on the complexity of the system whatsoever. They also do not provide any insight into the intrinsic biological plasticity and dynamics of the system.