Microbial Time

Science likes to use clock time to demonstrate that the life of the individual is nothing, and that human experience, in particular, when measured against the immensity of the universe and eternity, is not significant. And I suppose you can’t really blame Science for that, because it doesn’t have any other option other than to work with clock time. Clock time is necessary for making precise measurements, Science relies heavily on being able to use the metric of seconds and minutes. But we know, as human beings existing through lived experience, the life of the individual does, in fact, have great impact, and that human experience is not trivial or insignificant.

Humans perceive the clock as regular, and uniform, but clearly, living a life isn’t like that. Our time is not even, and actual existence is a collection of events and experiences through which we live. Living, being alive, describes the passages of time according to those events, whereas clocks assign value to hours and seconds, arbitrary productivity standards such as the Monday-Friday 9–5 work schedule which has obvious links to us donating our bodies and energy to capitalism. Because clock time is an abstraction from time as we live it, this creates confusion around who owns our days. As a tangential example, it was interesting in the early stages of the COVID-19 pandemic to watch folks demand to know when it would be over: the need for a date and a time that they would be delivered from it. Internet memes at the time suggested that people wanted to speak to SARS-CoV-2’s manager.

Eternity, or notions of divinity, can vanish with this flavor of time. But is this loss unique only to humans?

After all, biologically speaking, many different kinds of metabolisms are driven and maintained by the presence of tiny cellular clocks. Examination of circadian rhythms has revealed that the majority of Life with a capital ‘L’ is in sync with the rotation of the earth via relationships to sunlight. Clock proteins, in organisms with life spans longer than a day, are made and broken down in 24 hour iterations. Plants seem to exist much more slowly than we do, but to them, an hour is still an hour, a second is still a second: there is temporal succession.

Within the microbial universe, these ideas are nuanced. In many cases the ability to track biological time imparts evolutionary fitness, but in others — why follow a 24 hour clock if you don’t even live that long? The reason why plants seem to live at a slower pace, physiologically at least, is because they’re not motile. They rely on the production of poison or spikes or team work or sacrifice to defend themselves, instead of running away. They don’t experience explosive or radical turnover in energy the way a cheetah does, they don’t migrate to mate or feed. They are not bound, they still move, they just mostly move in the same place as before.

But how do not-humans perceive time, truly? Particularly when they’re ancestrally linked to the very beginning of life? It might make more sense intuitively, when journeying with a plant to try and slow one’s self down to plant time. But the microbial world represents numerous versions of time, branching off in several different directions at the same time, god help us all. The universe is expanding but it’s not expanding into anything, and as humans learn more and more about the smalls, it’s a similar phenomenon. They are the foundation for the present. They are outside of time at the beginning, and they are outside of time at the end. But, within ourselves, they are present ubiquitously throughout our human ancestral lineages, and because of their presence on those lines we have knowledge of medicines and agriculture and beer and cheese. Even more than those external signatures, the very cellular pieces of us that allow us to convert food to energy, to exist, that connect us physically to all our grandmothers, were originally, probably, co-opted microbial lives. The smalls also force us to delineate our sense of self from the rest of the living and dying world — they’re a finger smudge between the charcoal boundary of our physical meat-sacks and ‘Everything Else’. Within that ancient finger smudge though, too, are tiny units of life that rise and die in very small incremental time-frames — a few hours, twelve hours, then dead.

There are lines of laboratory strains of bacteria that have been maintained for years. Assuming that you don’t care about mutation or contamination for a second, you could argue that these cell lines represent a kind of immortality. While many are dying, a balance is met which dictates that many are also being born simultaneously, and providing these domesticated ones are tended to by their human keepers and offered food and a means to remove waste, they could go on living indefinitely in their tiny plastic containers. However, this immortal community is populated entirely with aging and dying individuals, and when a bacterium divides the two daughter cells are not born equal.

If we assign polarity to a rod shaped cell which subsequently divides, it stands to reason that there will be ‘newer’ ends of the cell and ‘older’ ends of the cell. If you assign a new pole and an old pole different colors and then keep up with the numbers of times each end ultimately divides, and how many new and old poles are produced, from the original cell, it’s gets complex very quickly (as everything tends to with exponential growth). When you track this ‘age’ as a function of decreased metabolic activity, decreased fitness of offspring and greater chance of death we can see that this community, previously thought to be clonal and functionally immortal, is in fact highly subject to the effects of time. Functional asymmetry within the community drives this process.

Within systems that rely on a dynamic microbial ecology (i.e. pretty much everything), the amount of time that any one microbe sticks around in that system also has a big impact. Microbial Residence Time, or MRT, exerts complex pressures on the diversity and function of engineered systems, the greater natural world and host-associated communities. There is some evidence to suggest that the longer the MRT, the more diverse the system and the more likely we are to observe specialized biotransformation like nitrification in wastewater treatment systems. But there’s that key balance thing, again — the turnover still needs to be fast enough to maintain an efficient, functional population which doesn’t drown in it’s own waste.

The Smalls don’t escape time, nothing does. And that deal is also known as Entropy. But, in maintaining entropy at the same time as imposing order on the community by gathering energy into the production of new cells, you could argue, still, that a curated immortal community is an immortal community nonetheless.

Eugene Koonin’s description of life in a post-genomic world is enjoyable and poetic: two empires and three domains, the two empires being viral and the cellular. The cellular world includes the three domains of life: the bacteria, the eukarya and the archaea. Archaea, we only really noticed in the last 40 years or so and made assumptions about them existing only in extreme and hostile environments. Now, we understand a little bit better that they’re everywhere. And they’re cryptic little beings. Uniquely, their cell membranes contain isoprene chains instead of lipids, allowing them to survive and grow at very high temperatures. Archaea are also the sole lifeform (that we’re aware of) who can perform methanogenesis. In environments where no oxygen is present, methanogenesis is one of the final stages of organic decay — and so the archaea are responsible for the release of considerable amounts of carbon in anoxic environments. Aside from interest in their contemporary activities, their capacity to survive up to 125 degrees centigrade and produce methane makes them an interesting tool in the study of early earth history. Modern-day archaea likely represent an ancestral lineage that was present on earth back when conditions were hostile to most life. And their relationship with the eukarya suggest they may provide us with clues regarding the crossover between prokaryotic and eukaryotic life. Archeans contain some genomic homologs which are more similar to eukarya than the bacteria — some are even exclusively shared only between those two domains.

But this work moves slowly and is extraordinarily difficult to perform because archaea are hard to find and even harder to grow in the laboratory. A group of microbes known as the Lokiarchaeota, members of the superphylum Asgard archaea, falling inside the kingdom Proteoarchaeota, are now thought to be our most likely bet for hints about how the move into eukaryotic life occurred. It took researchers five years to grow them in culture, and their doubling time is two to three weeks: two to three weeks to luxuriate in the process of cell division.

So there’s a lineage of smalls that may have brought the whole of multicellular life to where it is today: a truly ancient ancient ancestor at the head of that table. A long time to get here, still a long time to get to where they’re going. Life in slow motion — slower than the planets, maybe? There’s no rush when you eat carbon to make methane. When you’re the final stage of organic decay. That’s clearly a different version of microbial time than the highly resolved molecular increments we were previously discussing.

So within all of this information, knowing that time in the microbial world is both glacial and lightning fast in pace, how do we reconcile ideas of eternity and other directions of time for our human selves? It is really difficult to perceive the point at which microbial became multicellular, or even when the microbial came into existence — because these events are almost completely inaccessible to us. They’re beyond time. Science can take a stab at a guessing what happened but we’ll never completely confirm it to be true.

There are analogs for the relationship between the microbial world and time, and the relationship between God (or spirit, or whichever way you wish to frame that) and time. Is the microbial world, in fact, timeless and beyond time in the same way that the most crucial events at the beginning of life are? The contemporary microbial universe, and all ancestral lineages therein, are arguably everlasting but they have experienced and do experience temporal succession in as much as Tuesday came after Monday, and Sunday came before Monday, and so on. We see this as we watch them being born, growing old, and dying, voyeuristically through our microscopes and plastic-sided flasks. However, as far as we are concerned, from humanity’s perspective, they never began to exist and they will never go out of existence. First to evolve, last to die. Members of two out of the three domains of life encompass all levels of time, then (and also, those members of eukarya that possess more microbial-than-mammalian attributes, for example - maybe giant trees or yeasts). Doubling times of twenty minutes, doubling times of two to three weeks. There at the beginning of time, evolving response to massive, and massively slow, necessity.

To examine another aspect of what this means in the microbial world we should return to the idea of ecotypes and labels, and the microbial response to pressure. In the same way that so many humans rely so heavily on clock time, since we first started formally engaging with the natural world, we’ve been giving stuff names. Our ancestors had names for plants and animals, features of the land and skies — but since we’ve really only just recently found out what microorganisms are, they probably didn’t recognize bacteria and viruses specifically. While there have been lots of names for and deities associated with disease and specific diseases, our people didn’t necessarily know, biologically speaking, what caused them. The concept of ‘modern’ taxonomy, a systematic way to classify living things was first introduced by a chap named Carolus Linnaeus. Linnaean taxonomy is based on obvious physical traits, and the similarities between those traits across different groups of botanical and zoological beings. Linnaeus started this work in 1758.

Unicellular organisms (like bacteria) were initially described in the 1670s by by Antonie van Leeuwenhoek, using a microscope he designed. Van Leeuwenhoek is considered to be the father of microbiology, and he named his new discoveries diertjes (Dutch for ‘small animals’ and translated back into English as ‘animalcules’). Later, as more people began to observe and study microbial life, formal classifications were applied on the basis of cellular shape and external features and the naming conventions followed those dictated by Linnaean taxonomy whereby latin names were assigned to everyone: Homo sapiens, Cathartes aura, Vibrio cholerae. Names for specific genera of microbes were introduced, ‘Vibrio’ in 1854, ‘Bacillus’ in 1835, ‘Spirochaeta’ in 1835.

But the sheer abundance and diversity that we observe throughout the microbial domain today renders these classifications, at times, very unhelpful. The genus Bacillus currently contains 266 named species, all of which look pretty much exactly the same under a microscope, but exist and perform in a huge range of environments, from the arctic to the Atacama. Therefore, in 1987 Carl Woese divided bacteria in 11 broad divisions, based on the DNA sequence of the ubiquitous 16S rRNA gene (incidentally, while he was doing this, he also argued the point that archaea belonged in a third domain, and that’s why we’ve got three domains to consider now). However, the more we learn, the harder is becomes to define the fundamental units of bacterial diversity, particularly those that cover both taxonomic and functional operational units. For example, a Bacillus found in the soil of the desert may fall into the same species as one found in Antarctica, but they’re not interchangeable. If you switched locations, they’d almost certainly immediately die. Environment favors adaptability, and there’s no simple answer to how that happens coded in the 16S rRNA gene. So, on top of genera and species, we can also talk about ‘ecotypes’ of bacteria.

Naming microorganisms, while a very human pursuit, is incredibly difficult because, aside from representing a huge amount of genetic diversity and abundance, microbes exist as a kind of hivemind and are also constantly dynamic in terms of age and activity and the associations they make with other organisms. In any given place there may be hundreds of interacting taxa: and the abundance and diversity of those taxa affects the activity of that place. So, you can see why it’s a bit reductive to say: this is E.coli and E.coli makes you sick.

Pressures from outside environment led to evolving traits which may behave very differently from those of the ancestors, and that makes sense because this all this happens very quickly in the microbial world. Adapting when you have a simpler structure means evolution happens much quicker and it’s not difficult, for example, to train viruses to infect a broader range of hosts in the laboratory — so imagine what it’s like outside, where the whole wide world can get to them. The point is — temporally, spatially, the microbial world is not static ever, at all, regardless of how we chase it with little nets and collecting buckets and labels. That universe encompasses aspects of structure according to the passage of time and the delineation of physical space, but simultaneously rejects all of that as well. It’s simply inconceivable, impossible, that you could scoop up two handfuls of sand from the same spot within the frame of a millisecond and say “these are the same”.

The the inner life of the microbial world is then, at first glance, sequential and temporal, but in relation to human temporality it might be geologically slow or very very fast when considering rates of reproduction or a cellular clock. Their time is distinct from ours and only crosses over with our own at certain points. It is possible, like God, then, that microbes are omnitemporal. That they have no intrinsic metric beyond their lived experience in relation to the rest of the planet. And that we assigned a much narrower definition of temporality when we started looking for them and watching what they did because we use science, and science almost entirely dependent on clock time.

We have urgency when it comes to ending a pandemic or training fungi to eat oil spills, but a small part of the reason this kind of techno-solutionism isn’t going to work is because the microbial world operates on a different temporal basis to humans. And when we try to manipulate them into our version of temporal succession, that’s unsuccessful, obviously, because humans can’t manipulate our own time, let alone the time of the most ancient and newest organisms to inhabit the planet.