It may be that, in Shinto Buddhism (the predominant religion in Japan,) the "ghosts" of microorganisms, insects, etc. don't exist, or aren't worth worrying about, because they're part of the natural order.

Also bear in mind that, if one believes in reincarnation and animism, "ghosts" on earth may be considered a special case, when the expectation is that most spirits rejoin the karmic cycle (or whatever.)