Everything is made of matter, matter can be affected by physical waves, and viceversa. That is the soul, some sort of organized physical waves that in the abscence of its "original matter" can affect another instead. Everything has a soul, how could it not? Even rocks have a soul, since they are made of matter. What happens if I break a rock to pieces? Well I don't know, but I assume the physical waves affecting it are somehow still around, things don't just vanish, they merge with other things, that's how nature seems to work.
I don't believe in human supremacy. It's just a concept created by Christianity in Genesis that simply got catchy ( or maybe it's older, I wouldn't be surprised because of syncretism). Why is a human better than an ant in any sense? Because they are bigger? Because we can write and have technology? The ant doesn't need to be big, nor write, nor have technology, it's perfectly adapted to its environment as it is. We assume a lot of things about other species, but as everything we judge in reality, we do it from subjectivity. I don't know what is the spiritual life of a bee, I have no idea, I'm not a bee. Maybe they are incredibly spiritual, maybe they are greedy and selfish, maybe they experience life so differently that those concepts don't even apply. Do we say they don't have a soul because they don't have a personality that we can distinguish? Doesn't it make more sense that we simply don't understand them than that they don't have a soul? Not so long ago even certain human races "didn't have a soul" either.
Bugs get killed often? Certainly. Life is an exchange of "energy". For one person to live another day, plants and animals have to die. Nature eats nature, and stays in nature.