A lot of ethicists draw the line at either sentience (not sapience) or the ability to suffer, usually defined as the presence of a central nervous system. Bacteria fails to pass these tests.
Here's a summary of a paper in Nature about Bacterial perception:
http://biosingularity.com/2006/06/04/how-bacteria-sense-thei...
Better still is the communication, one example is quorum sensing. Bacteria sometimes take little polls before acting, like little mobs trying to rile each other up:
http://en.wikipedia.org/wiki/Microbial_cooperation#Quorum_se...
To the bigger point, putting an ethical line in here somewhere always struck me as a bit of a sorites paradox, the endpoints are fairly easy (don't torture humans, don't worry about bacteria), but there's no obvious line in the middle where you couldn't make an argument to include or exclude just one more species, especially when you confront the staggering biodiversity out there, and start to see everything as more of a spectrum and less discrete.
I avoid smarter animals, like pigs, squid, and octopi (dogs, cats, monkeys, or ravens if they ever came up). Cows and chickens are fair game. This is basically arbitrary, but I don't believe it's any more or less tenuous than anyone else's system, we're all making a call with limited information. (As Thomas Nagel put it, no amount of human thinking reveals what it is like to live as a bat.)
How do we define "suffering"? Is it the same emotional experiences we call "fear" and "sadness", i.e., the ability to have the concept "I am afraid/sad"? That means the animal needs to at least have a primitive form of understanding and introspection to qualify (e.g., great apes, chimps, bonobos).
If we go to the other extreme, we must admit we don't have a reliable method for communicating with animals (famous "dog whisperers" aside). We can only infer "suffering" is taking place when the animal reacts negatively to a negative external stimulus. But bacteria respond negatively to a negative external stimulus as well. Sure, there's mind-bogglingly more complexity in a mammalian brain than a bacterium, but if we reduce "suffering" to the observation of a negative reaction to a negative external stimulus, we must say even single cell organisms are "suffering."
Hard to strike the right balance.
[1] http://en.wikipedia.org/wiki/Plant_perception_(physiology)
[2] http://en.wikipedia.org/wiki/Inducible_plant_defenses_agains...