I agree with you Graham that for organisms like bacteria or insects it becomes difficult to discuss whether these organisms have intrinsic value. However, I have a hard time with applying “essences or a set of essences,” especially if they are to be a certain property that something possesses.
In respect to the “essences”, if it is something the organism is to possess, like as you state, a “physical, function, or potentially immaterial” property, wouldn’t labels such as these only help us sort out what type of instrumental property the organism has? For example, let’s say that it was determined that insect X had a specific role in its ecosystem, like decomposition of animal Y’s remains. I am assuming then that the property or essence of insect X would be: decomposer of animal Y. However, such a property seems to only designate what insect X does, not what makes it insect X. To me this is like saying that I am a human because I can talk, read, and write, but I am sure that you would agree that this is not what makes me human—these properties are not what make up my intrinsic value or even essence.
Also, there are some general problems of essentialism (which are why it is not generally accepted today). One, to ascribe an essence to a certain species you must ensure that all members of that species have that property. So what happens when a member of that species does not have that property or trait, are they then a member of a different species? Do they make up their own species? Second, properties may be very similar between different species (or even exist in other species). For example, a certain role or trait of a species may best describe its essence, but what if another species also has the trait?
In general, when it comes down to organisms like bacteria and insects; I think that it is more about respect such organisms through respect for each ecosystem as a whole. For example, if I make sure to not overuse and to reuse things that I need, and that I do not stomp around doing whatever I please and using whatever I wish (and along with other actions), I would say that I am respecting other people and other species around—and in general my surrounding ecosystem. So, in terms of biodiversity, by respecting your ecosystem (and thus the other organisms/species in your ecosystem) you are then helping in the conservation of biodiversity.