Competition and lack of nutrition are probably the main reasons – just like with any organisms, and to a much lesser extent inhospitable environments And like myth said, other species are capable of defending themselves. For example, some eukaryotic unicellular organisms eat bacteria, and bacteria compete for nutrients against one another, as well as against other microorganisms living in the same ecological . For example, many molds secrete substances that kill or inhibit bacterial growth. Even if there wasn’t any direct competition by other organisms, bacteria couldn’t "take over the world", if by that we mean that they’d cause the extinction of all other life forms and would be the sole survivors on this planet: there’d always be lots of habitats that are inhabitable for bacteria – mainly very dry (or cold) places, where vegetative bacteria survive only when living as symbionts or parasites on multicellular organisms that can survive there. So in other words, even if bacteria could rid the world of other living creatures, it would be against their best interests in many cases, and thus natural selection wouldn’t direct their evolution that way.
