For what reason(s) do humans rule other species and do those reasons apply within the species?

Because we decided to do so. Just as we decided that we are superior to all other terrestrial life forms. And rocks.

I think one group of organisms that has been left out of this discussion is bacteria. While they are by far the simplest form of life, because of their ridiculously fast exponential breeding they evolve much more quickly than anything else and can learn to evade our defenses.

I posit that humans haven’t really “conquered” bacteria. Sure, we have sanitation measures now and to some degree have drugs to target bacteria, but in many cases we already see many bacteria evolving resistant strains, and doctors have to be very careful to give antibiotics targeted specifically to a patient’s infectious flora, because giving broad-spectrum antibiotics will only lead to greater resistance.

And while most of us could imagine all of humanity being killed by a species or genus of bacteria, it’s pretty impossible to imagine humanity wiping out all Staphylococcus, for example.

Yeah, I think you are being a little metaphorical for this thread.

Fact of the matter is that humans (and animals) have certain physical needs - food, water, shelter, so on and so forth. If one person or group has control over the acesss to the resources that provide those needs, they have power of those people who don’t.

Not only are we the only species that can “decide” that we are superior, we are the only one who can build tools and weapons and alter their environment to enforce our superiority.

because we have nukes and the animals don’t

I know that is meant to be a somewhat joke answer but there is a touch of brilliance to it.

Ask a regular person what is more evolved, humans or a cockroaches? Almost all will say that humans are but that isn’t true in the least. Humans and cockroaches have been evolving at exactly the same rate on the earth animal tree. Cockroaches just got really good at it fairly early so they don’t need to change much over time to adapt to circumstances. Humans as a group are pretty impressive with the amount of successful genetic adaptations we have had in the blink of an evolutionary eye but that doesn’t mean that much because we are still a fairly vulnerable species.

Humans can mostly be wiped out fairly easily by internal or external forces but that isn’t true for lots of other lifeforms. Cockroaches are really impressive biological machines that can survive just about anything as a group and we can’t I doubt they are very impressed by our poetry and paintings.

I asked my cat if she’d like to be in charge, and explained that this would mean going out to work so she could provide for all of us.

She said “meh”, rolled over, and went back to sleep.