Do unique communities of bacteria form inside water storage in plants?
As stated in Plant Signal Behav. 2010 Dec; 5(12): 1568–1570:


  Phytopathogenic bacteria do not enter plant host cells, but proliferate in the intracellular space. 


But as they can reach the apoplast, pathogenic bacteria can take advantage of environmental humidity levels and manipulate water content inside plant leaves to reproduce and spread infection as shown in
Nature volume539, pages524–529 

So yes, bacteria can infect water inside plants but usually not inside the plant cells themselves. As they infect the intracellular space, they can spread in the water and infect the whole plant. It is also to mention that we are not speaking about the same bacteria as in standing water or something else. Viruses on the other hand can infect the plant cells themselves.