Why microbes?

In order to gain a deeper understanding of why microscopic lifeforms are so important to the existence of life in general, we need to begin with the fact that these were the very first life forms.

Not only did all other forms of life develop from them, because they formed the initial communities from which all further developments in life evolved, all these developments in life ultimately built their livelihood directly on the foundations laid by this community of organisms.

Growth depends on the acquisition of nutrients, and in any given environment—especially, perhaps, the most primitive ones on early earth— the total amount of nutrients is quite limited. It furthermore always costs something in terms of energy to acquire nutrients and concentrate them. This is what microscopic life — the first cells — did. In doing so, they created richer, far more concentrated repositories of nutrients.

It turns out that one of the best ways to acquire richer sources of nutrients is to exploit pre-concentrated ones that already exist—that is, steal them, which usually takes less energy than doing the work of concentrating them. And indeed, very early on, lifeforms began not only to compete with each other for the available raw nutrient resources; they learned how to take them from one another. In other cases, they learned to cooperate with one another and share resources; but in either strategy, it became expedient to lock the nutrient resources up in one way or another so that they couldn't be easily shared or stolen. The idea was to make the cost of acquiring these richer sources of nutrients – that is, the bacteria themselves – high enough that it wasn't worth it to others, unless they were willing to give something in return. That could include anything from a mutually beneficial exchange of valuable substances up to the taking of the other party's life in order to get what they had. Cooperation and competition.

Locking these nutrients up took two obvious directions. One of them was to develop body shapes and forms that had strong defensive capabilities. Groups of cells cooperating were better able to defend themselves than single cells; and so one of the first steps in life was the advent of cellular communities, which developed into what we now call organisms. The organism is the microbiological equivalent of individuals and societies banding together to form an army. Communities of cells were better able to defend their resources; they were also, it turns out, better able, in many instances, to acquire them. It wasn't long, in fact, before they began actively altering the environment around them to favor their survival. This took a number of forms—still with us today—which we'll talk about later.

The second line of defense for nutrient resources was to lock them up in chemical forms that couldn't be used by adversaries. One of the best examples of this chemical defense mechanism is cellulose, which is incredibly effective at taking nutrients and locking them up in an unavailable form. It works so well that almost every plant on earth now builds its life around the production of cellulose. This has forced the many larger organisms that want to feed on it—after all, it is incredibly abundant!— to develop mechanisms that can defeat the chemical "locks" on cellulose by digesting it.

The mechanisms that allow animals to digest cellulose are all primarily microbiological. Because it's difficult to attack cellulose in any other than a chemical way, digestive juices of various kinds must process it, all the way from the macrobiotic (gut) level to the microbiotic (fermentation) one.

Despite several billion years of evolution since the advent of the first single cell organisms, everything on the planet is still arranged in exactly this way. Cells lock nutrients up to make them unavailable; and animals and plants which choose to acquire them have to use chemical tools to unlock those nutrients. Even the largest creatures with the biggest teeth and the most powerful muscles can only do the initial job of acquiring the foods; microbiotic forces have to unlock them and make them available. And in the vast majority of cases, in fact, probably all cases, larger organisms have recruited their own colonies of microorganisms to help them do this. (The whole process of decay is deeply tied to this activity.)

This means that when you get a meal for yourself, the meal isn't just for you. It's for the microbes in you as well; you need to feed them, or they can't feed you. Eating the wrong things for them will ultimately lead to bad results for you as well, because it will favor the development of microorganisms that aren't beneficial to your digestive process.

Although forms and sizes have changed over billions of years, the fundamental underpinnings of the food chain have never changed. Given the strong persistence of DNA throughout life as we know it, it's very likely that not only DNA, but also the nutrient-storing molecular forms it encodes for, are much the same as they were billions of years ago. We know, for example, that there were plants of one kind or another using chlorophyll that long ago. They are still doing it today — and so we exist in an unbroken chain that relies on chlorophyll and its molecular productions for energy. Without it, sunlight couldn't be converted; and without the sugars that it converts molecules into, pretty much nothing on the surface of the planet could live. (There is, of course, another chapter to this story—creatures under the surface.)

In a certain sense, then, microbes are running the show; all of us are just vehicles for their action and dispersal. The more efficiently an organism interacts with the microbial community it supports, the more effectively it competes in the acquisition of nutrients. So the microbiological community actually fuels the process of evolution in ways that are still not well understood.

Because of our general ignorance in these matters—and the impression that we can do little or nothing to intelligently manage such things—we have, on the one hand, blithely ignored our relationship with microbes and, on the other, attempted to exterminate the ones that we know cause disease. Both approaches have turned out to have their drawbacks; the one, because we cause harm we don't know about, and the other, because our short-term management of infectious disease in both livestock and humans has led to unforeseen problems in microbe evolution.

Microbe evolution is taking place all around us, all the time, and at a much more rapid pace than our own. 

We'll take that up next.