About Microanimism

Adventures in relating with the smalls

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Microorganisms are, to a select group of human people, a very charismatic group of beings. Encompassing the bacteria, archaea, fungi and viruses, an entire sub-discipline of biology (‘microbiology’, or ‘microbe-biology’) is dedicated to studying how the very small folk on this planet exist and thrive. As a microbiologist, I’ve been studying microbes in the environment for almost 15 years.

Everything begins and began with microbes.

False color image of muscle. The red spots are mitochondria - small features of a cell which produce energy. Current endosymbiotic theory suggests that mitochondria were originally bacteria, who took up residence in cells 1.5 billion years ago (as far as we can tell, based on the fossil record).

False color image of muscle. The red spots are mitochondria - small features of a cell which produce energy. Current endosymbiotic theory suggests that mitochondria were originally bacteria, who took up residence in cells 1.5 billion years ago (as far as we can tell, based on the fossil record).

The large life on earth, as we understand it, began after a group of microbes polluted the early atmosphere with oxygen, allowing for aerobic (oxygen-requiring) growth and the appearance of more complex organisms: animals and plants. These groups developed cells containing membrane-bound compartments, which provided the division of labor required for complex and simultaneous activities and metabolisms. Their DNA became enclosed by a nucleus and they grew larger, developing adaptations and specializations. As time went on, highly specific symbioses were bartered between the small folk and the larger folk, and microbes took up residence in the complex cells of mammals and plants, allowing for aerobic respiration and photosynthesis.

A microbial mat at the Grand Prismatic Spring in Yellowstone National Park. The beautiful colors arise as a result of the activities of pigmented microbes, who are adapted to live and thrive under the extreme conditions of their environment.

A microbial mat at the Grand Prismatic Spring in Yellowstone National Park. The beautiful colors arise as a result of the activities of pigmented microbes, who are adapted to live and thrive under the extreme conditions of their environment.

Many of us understand, perhaps on a very primal level, that plants are the human species’ conduit from the sun – without green plants we wouldn’t have the oxygen we need to stay alive, and the valuable source of food that plants represent. But microbes deserve credit and recognition for being the first to receive and use sunlight in this manner, and for delivering that capacity to the green plants of today. Photosynthesis is a cosmic waltz, performed at every level of life: celestial (the process requires photons from the sun), organismal (light is received by specialized groups of creatures), cellular (centers of light utilization are located within each cell), subatomic (photons excite electrons in the light processing centers, starting a cascade of energy transfer which ultimately produces oxygen and sugar). Microbes brokered this deal.

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So, undeniably, microbes have an ancient relationship with the planet, and they have been with us humans since we showed up on the scene. I’ve noticed, since the start of my career, that humans seem to have become a lot of more comfortable with the general concept of microorganisms. There’s not so much of an ‘ick’ factor. Recent work has demonstrated why we should treat microbes as an additional human organ, and there is much to be said for understanding the microbes that colonize our bodies – they’re as unique to every person as their fingerprint and wherever we go we leave a microbial signature. However, scientists are very far away from understanding human-microbe relationships comprehensively enough to manipulate them. Interventions for example, for obesity and diabetes are potentially on the distant horizon, but not yet within our grasp. We just don’t understand enough about these communities of microbes. I think we have little true fellowship with them.

There are many offerings on the market allowing you to ‘meet your microbes’. Kits and bottles that are sent through the mail will tell you the bacterial composition of your gut, or your cat’s gut, and will offer insight into your own nooks and crannies. Or, you may wish to send out your stool as a charitable donation, to contribute to large citizen-based research projects. Perhaps, you are providing your sample for downstream use as a ‘transplant’: your gut flora, used to seed someone else’s sick or underfed piping.

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There is good to be found in all these activities, like digging through ancestral records when to you want to connect to your people. However, ‘your’ microbes: are not yours. They are very distinct living entities that have happened to agree that your gut, or skin, or lung, or mouth, at this particular moment in time, is a suitable and rewarding environment to live in. They are not ‘bad’ and they are not ‘good’, in the same way that there are no ‘bad’ or ‘good’ bees buzzing in and out of the tree in your yard. They perform esoteric, highly specialized activities which no other living thing can do, activities that scientists are very far from understanding comprehensively, or at all - they are astonishingly adaptable, and they are overwhelmingly numerous on a global scale.

It is difficult for a scientist, as an animist, to connect to the very smalls. I think it may also be a challenge for a non-scientist animist to do this. Our ancestors, after all, mostly didn’t know about the very smalls. When humans first laid eyes upon them, via a homemade microscope, we spectacularly misunderstood what they were. We are endearing, that way. It can be difficult for any scientist to reconcile their feelings about nature or spirit with their professional and natural reliance on fact and logical, linear thought, and there is a primal, vestigial reflex towards the land, towards macrofauna. It is far easier to see medicine in Vulture, or Juniper, than it is to see it in the Ebola virus.

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So, why is it so difficult for microbiologists to separate microbes from the earth? Because microbes are the earth. Go outside and scoop up a handful of soil. Go to the beach and dip your feet in their water. Next time you have cause to, take a look at the root system of a plant, and know that in every microgram there are hundreds of thousands of microbes supporting that life, making that life feasible, helping it thrive. They do so benignly, just because: that is what they do. In the same way that we, as conscious (or unconscious) humans may feel cradled and held by the earth, the mountain, the plants or the animals we exist alongside, we should engage thoughtfully with the bacteria, viruses and fungi who broker the deals between the big life and the building blocks that create life - molecules, atoms, electrons. How to tend to and honor these relationships? Back in the earlier stages of my career I certainly developed something like a kinship with the organisms I was working with - and many other scientists would tell you the same. There's always one group you resonate with, or one person in the lab who is more skilled at working with a certain strain. Many of the microbiologists I have worked with have spoken of developing a 'sixth sense' - you just know when the bugs are happy and when they're not. You know what makes them tick, you know what pisses them off and causes them to grow poorly. Culturing microbes is an art, and relies heavily on intuition. Where does that intuition come from?