~ The Microscopic Appeal of 18 June ~

Yeasts, unicellular microscopic fungi (electron microscopy, Dennis Kunkel)*

They were here before us and will be here after us.
We can’t see them but they are everywhere.
We don’t know it but we owe them everything.

These unknown soldiers, these despised fellow travelers, are the microbes. Named after their microscopic size, they’re infamous for transmitting diseases and even for killing. They terrify us whilst only a tiny portion of their kind cause trouble. We are unable to conceive how huge the protective and creative power of these living creatures is. And how vital their existence is to us. As they act discreetly in the shadows, we endlessly fantasize about them instead of celebrating their exceptional contribution to life. Microbes shape all living beings and their relationships. They have nothing to envy to the Olympian gods. They are at work everywhere and their power is huge. Bacteria, viruses, unicellular fungi and other jewels of the microscopic kingdom, these « little lives » are great allies. Since the dawn of time, these ancestral terrestrial entities have offered us the secret and the power of energy, the mysteries of self-defense, the miracle of digestion, the recipe for fermented food, the virtuosity of biogeochemical cycles and so much more. They are infinitely small in size but gigantic in their influence on the lives of all the beings on Earth. It is by roaming this microcosm, by taking in all of its boundlessness, that breaches will open up in our imagination to help us consider what is to come in a more accurate manner.

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When we talk about the ecological crisis or the biodiversity crisis, microbes are rarely mentioned.And yet, they play a crucial role. They are invisible but they do determine what happens to all living beings and to the cycle of matter. At every level, they weave and unweave the web of life. Microbes regulate ecosystems, modulate the flow of carbon and nitrogen, create symbiosis with all living beings, protect against pathogenic agents, facilitate nutrient absorption, educate the immune system and regulate a great number of physiological parameters.

No living being could live without its troop of microbes. They have forged intimate and unbreakable bonds with each species. In the intestines, on leaves and appendages, in the mouth and on wings, in pistils and between the toes, on the scales and hairs, on the abdomen and in the roots, in the eyes and reproductive organs, microbes have adapted to every eccentricity of life. Whatever scale we look at, microbes are at work. Our cells are even inhabited by the distant memory of a symbiosis with bacteria that brought us the secret of energy production (2).

These tireless cosmopolitans have ventured in the most extreme places, from the bowels of the Earth to spaceflights. They have survived every disaster, put oxygen in the atmosphere, seen the extinction of the dinosaurs and the rise of the first civilizations. They are the first to welcome us at birth and the last to care for our bodies by re-integrating them into the landscape and into other life cycles.

However, is there any life-form more despised than microbes? Within our tongue live billions of microbes and a misunderstanding. We discovered them at the very same moment we understood that they were responsible for some diseases. We baptized them with a name that from the beginning bore the seeds of a disdain made to last. The word microbe literally means « little life » (from the greek mikros « little », and bios « life »). It is therefore not tinged with negative content in itself but its use has made it drift towards a negative connotation. I prefer it to the more neutral term microorganism, which means the exact same thing, minus the negative prejudice. To use the term microbe is to face our assumptions and to try to get rid of them. It’s also assuming that there is still a misunderstanding that needs to be unravelled in our collective imaginaries.

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They’ve been part of all the battles and will, once again, be one of the key elements to planetary equilibrium. The impact of major upheavals will pass through the microbe’s prism which represents the huge majority of earthly life-forms, both in terms of the number of individuals and their diversity (1). The salvation of all other living beings largely depends on the survival of microbes. When we talk about biodiversity, we think about bees, whales, polar bears and swallows but microbes are very rarely mentioned. They aren’t hung as posters in the children’s room. Yet without overshadowing other creatures, microbes could easily make us dream if we changed our outlook on them and if we contemplated their incredible kingdom. By their almost magical powers, their mystery, and because they reside in the invisible, they invite reverie and excite the imagination. Here, it’s not about downward competition with polar bears, but on the contrary, it’s literally about organic solidarity. It’s not one or the other, but one and the other.

Microbes can no longer be left out from our thoughts about the collapse of biodiversity because they are essential to each of the dying forms of life. When an individual’s microbial roommate degrades, it jeopardizes the existence of the super-organism in which it has exercised its powers. This is exactly what happens to bees: glyphosate primarily damages their intestinal microbiota, which can no longer protect them from pathogen invasions (3). We can experience it ourselves with antibiotic treatments. They destroy a part of our microbiota and can expose us to infections, particularly to the Clostridium difficile bacterium (4).

Microbes must be welcomed to sit at the negotiating table. Not because they’re endangered (by the way they don’t need us at all) but just because we need them. We need their expertise and their great dexterity. Our disdain and fears must be overcome, surpassed, to face together the important individual and collective questions that we need to solve.

It’s a question of sharpness, even if this focus requires a micron adjustment. To take microbes into account is to help us see the world with a filter, a microscope, which would allow us to access everything that is played out in the invisible. It is to refine our knowledge at a time where we need to re-think our ways of living, especially the way we coexist on Earth. We must now read between the lines, parley with the invisible and consider this missing link in each of our projections. Collaborating with the invisible requires scientific dexterity but also imagination. Who really populates the planet? Who is at work here and there? How can we imagine a future together? The perspective opened up by microbes should provide a stimulating contribution and a new way of thinking about all these rising questions. It is for all those invisible beings that I want to pay a vibrant tribute in order to make them better known, highlighting the intimate and decisive alliances we will have to build if we want to save what can still be saved.

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Of course, it’s hard to talk about this during a pandemic and to declare “Glory to the Microbes!” may seem provocative. It is however a great opportunity to finally become interested in them and to overcome our prejudices. We have to understand that microbes are in fact our allies rather than our enemies if we are to use the war metaphor that has been used to describe the crisis. We could even say that microbes help make things visible to us. This planetary rash is a particularly useful indicator for understanding that we have crossed the line, while the virus has crossed an inter-species barrier in the opposite direction.

Contrary to what we have heard here and there, this epidemic is neither pure chance, nor a human invention, nor nature’s revenge, but the foreseeable consequence of the way we inhabit the world nowadays.

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Microbes constitute a huge majority of the living. There are more microbes species on Earth than stars in our Galaxy. We count about a thousand billion microorganism species upon only ten millions of animal species (6).

They are precursors, they have shaped the world from the very beginning. They’ve set the parameters which other living things have to live with. These organisms are the puppeteers of all of life on Earth. They are hidden in the invisible, like a director observing what is played on stage, relentlessly, without intermissions. As the performance progresses they are modifying the backdrop, the setting, the acting and apparences, sometimes radically with the elimination of certain roles.

Microbes can be found in the most unexpected places, in environments where no complex life can resist such inhospitable conditions. Unlike other living beings, which live on a very thin layer of the Earth, microbes can be both in the highest altitudes and in the depths of the soil. Every day and in every square meter, in the troposphere of the sky we can find billions of viruses and tens of millions of bacteria that can fall back with the winds, sandstorms and rains (7). They are also found in the bowels of planet Earth at a depth of several kilometres, where they form an intraterrestrial life, that is quite staggering, since they must derive their energy from the weathering of rocks.

The Earth carries life in its acidic, burning, obscure places as much as in its gaseous envelope, which is transparent to the naked eye, but densely populated by microscopic life. Through their trajectories in the air and under the Earth, microbes draw the convolutions of an invisible migratory people taking full advantage of the geological dynamics to rush into them.

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Somes microbes have established themselves within living things.

Thus, a deep and intimate pact unites them. Microbes weave invisible networks that connect the beings to each other, in life and death. They are both our ancestors and contemporaries, our parents and cousins. They are within us, they live in the depths of our intimate territories, even in our cells. Day and night, without interruption, they are making us plural beings, overflowing identities, semi-human and semi-microbial. Our true nature is swarming and bickering.

Humans know since Copernicus that they’re not the center of the universe and since Darwin that they’re not at the peak of evolution. They’ll now have to live with a new narcissistic wound: the human being is not a single entity but the meeting of countless other species without which they couldn’t survive. They are not the only master on board, like the ship’s captain. They can no longer say “who”, of themselves or of the microbes, hold the rudder. Thus, microbes shatter the dogma of the one and only pure organism.

Whether we like it or not, we have extremely numerous and extremely intimate relationships with microbes: each living being has its own escort of microbes, its own microbiota that it largely inherits at birth from the mother’s vaginal microbiota and during breastfeeding. In the case of caesarean birth, the microbiota is composed differently, probably with increased susceptibility to allergies and other disabilities (9).

We now use the term a “holobionte” (10) instead of “an individual”. In other words, we talk about a host and its procession of microbes. Even on a purely metaphysical level, microbes contradict this period of time when nations are withdraw into themselves, erecting borders and exacerbating feelings of identity. Microbes teach us that purity doesn’t exist. This fantasy is deadly because it is sterile and because we would be incapable of living without them. Life is a continuous contamination. The stranger is within us, whether we like it or not. The microbe introduces us to polyphony and turn chimeras into reality.

If we look at the cellular level, we have as many human cells as microbial cells. But if we look at the genome level, and because the microbes that populate us are very diverse, the majority of our hologenome is microbial! This hologenome is like a marble veined with millions of streams each carrying a genetic identity. And if we look closer, each of these streams is itself a torrent fed by thousands of affluents inherited from all our ancestors.

Ghostly microbes have persisted in each of our cells as the vestiges of a far past where they came to find refuge within us. In exchange they’ve produced the precious fuel that still feeds our cells. These ancient bacteria have become organelles called mitochondria, the units that produce our energy. In plants, in addition to the mitochondria, other microbes have become chloroplasts, the organelles that enable them to produce energy from the sun! These endosymbiotic idylls illustrate the interdependence and intimacy that have always linked us to microbes.

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Of all microbes, viruses are probably the most feared. The word virus clearly attests to this since vīrus refers to poison, venom. The metaphor of computer viruses and the current situation have only reinforced this aversion. Here again, the picture is misleading because we owe a lot to viruses, those powerful entities that do not only bring disease, far from it.

Viruses shirk from the outset. They escape all attempts to classify them. They are the clandestine passengers of life that we can not control or regularize. They are cross-border beings which cross all borders, wandering from one cell to another, from one body to another, from one species to another.

Are they alive? The quarrel remains (11). At first glance they are not as they do not have the great characteristics of the living, notably the capacity to replicate with their genetic material. But their immense contribution to life and evolution, as well as numerous discoveries, disturb these categories and force us to reconsider the image we have of life and the very process of evolution. As usual, viruses seem to be able to break boundaries and categories. In particular, they are forcing us to re-think the phylogenetic representations that explain the story of kinship between species. These stories are still told without taking into account everything we owe viruses, these goldsmiths of our genomes, these foragers and nomads of evolution.

Darwin would have been shocked to see how viruses are slashing his famous tree of evolution (which he himself saw more accurately embodied by coral), how they append and tie themselves to it.They are the chief arboriculturists of the tree of life, they prune it and rearrange it incessantly. They fade away in front of this involuntary art work that they somewhat inhabit. Still invisible in our representations of kinship between the living, they are nonetheless the sap.

We have to imagine the virus as a kind of compulsive collector, a kleptomaniac that is a little absent-minded. When the virus infects a cell, it sometimes takes DNA pieces of its host. The virus may just as well forget its own fragments, which will sometimes become part of the genome of the infected cell. Sometimes these fragments are precisely those awkwardly borrowed from the previous species. This is how pieces of DNA from one species can travel and end up in another. This latter may die from it, use it, perhaps later, “when the time comes”. Haven’t you ever kept junk and thought it would be useful someday? The living do the same. And when living conditions change over time, fortunate are the generations that have kept in the attic of their genome the recipe, the right know-how to get out of trouble. Many things are useless in our genome. Useless now. But who knows what the future holds?

Life really works by successive contaminations. And the virus plays the main role since it is the most powerful vector of evolution, harvesting and sowing the contents of its booty throughout the living world.

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We inherited a lot from it. At least its many encounters with our ancestors have left traces. 8% of our genome comes from viruses. Amongst other things, this viral DNA contains the recipe for the placenta (12) which is an extremely complex tissue that allows food and oxygen to pass from the mother to the embryo. It also prevents the maternal immune system from attacking the foreign embryo. Viruses could also boast for having shaped our nervous system, stimulated our memory capacities, allowed the fusion between sperm and egg, opened the nuclei of our cells and so much more!

We mistakenly think that the lung of the planet is a forest and that only the plant world provides us with oxygen. In reality our lungs are oceanic because most of our oxygen comes from water, not only from phytoplankton (vegetal) but also from viruses. Almost all the biomass in the oceans is microbial and it is these invisible creatures that open up half of the oxygen on Earth! Each drop of seawater contains more than a million viruses (I’ll let you calculate the number of viruses swallowed when you drink a cup of water…). As real underwater orchestra conductors, viruses preside over the cycles of matter, kill some, release nutrients for others, and in the end, offer us this precious molecule that is dioxygen.

Breathe deeply, this fresh air is offered to you by those you thought you hated.

Viruses are part-time living beings

Recent discoveries bring viruses closer to the living’s ark. Some viruses can be infected by their fellow viruses (13) Others even have the superpower to create new genes (14) ! In any case, the virus doesn’t really care if it possesses a residence permit for the living kingdom. Whether one tries to put it to one side or the other, it seems that the virus taunts every category from its living-inerte border where it is walking like a tightrope walker.

“Personally, I’m non-binary” is something the virus could say. Perhaps its true nature lies precisely in its crossing-border ability, sometimes « alive » when it replicates a cell, sometimes « inert » when it is outside the cell and not able to replicate itself. It is a “transient microorganism,” say some researchers.

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The ecological disaster that allowed us to emerge

A disaster is not a disaster for everyone. We have clearly seen with this pandemic that in some areas it has allowed fauna and flora to redeploy where human activities previously forced them to retreat into increasingly narrow spaces. We owe our own salvation to the worst catastrophe of all times, the so-called oxygen catastrophe (15)! It was 2.3 billion years ago. Cyanobacteria sequestered carbon and released oxygen, which concentrated in the atmosphere at a rate ten thousand times higher than before. Yet, oxygen was highly toxic to most organisms at that time. This imbalance caused one of the biggest mass extinctions, mostly all the living have succumbed to the « bite » of oxygen. Some of them managed to survive and their metabolism got greatly improved by oxygen. Breathing organisms took precedence over fermentation organisms, and increasingly complex life forms emerged. Ozone, which is derived from oxygen, appeared and helped the beings to protect from solar radiation. This is how aerobic life, to which we belong, was able to develop on the ruins of a world that did not have the opportunity to invent the rest of its strictly anaerobic life history. Who knows what organisms would have looked like today?

Cyanobacteria didn’t have any moral responsibility to cause the mass agony of anaerobic living organisms by emitting high concentrations of oxygen in the atmosphere. But when humans pollute and intoxicate the air, soils, oceans and enslave human and non-human lives, they have a responsibility. Not only because they are aware of it. But also because they can do differently.

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Life isn’t in danger but the living beings are

A new disaster is looming. Perhaps as ferocious as the oxygen disaster. This time it is predictable, we see it coming and we have the means to stop it. But even if our survival depends on it, it is not absolutely sure that we will be able to stop it. In this case the planet will not succumb. Earth will continue to revolve and other creatures will start to rule, other evolutionary paths will take over, as when aerobic life rose up on the void left by anaerobic life. In that time this life-form was asphyxiated by too much oxygen, when we are instead starting to suffer from carbon dioxide excess.

Life is not endangered. It never has been, not even in times of mass extinction. It’s the living beings that are in danger. Other living beings will manage to live with what was unbearable for us and our kind. There is no ecological niche that empties without newcomers taking over it. This is the incredible tenacity of life that never gives up. We, humans, have to accept that other living beings will probably reign after us, on the ruins of our civilizations, and that they will take advantage of what has caused our loss.

To live not as gangsters but as cosmos gypsies

Multicellular organisms will be the most exposed, the most vulnerable. Unicellular life, on the other hand, has always been the most resilient. One has to believe that if microbes have started it all, they will certainly end it if we do not learn to dance in rhythm with other living beings. Even when the Earth will be destroyed by the Sun, in a few billion years, and will therefore no longer be habitable for any life-form, life will find a way.

Microbes won’t surrender. They will probably just run away. Small regiments have already scattered in the universe thanks to spaceflights. Outer space, inhospitable for us, is just another home for the gypsies of the cosmos, that are the microbes.

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“Microscopic animalcules” (Magasin pittoresque, 1833)*

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References

(1) https://www.journals.uchicago.edu/doi/10.1086/693564

(2) https://www.molbiolcell.org/doi/full/10.1091/mbc.e16-07-0509

(3) https://www.pnas.org/content/115/41/10305.short

(4) https://pubmed.ncbi.nlm.nih.gov/23478961/

(5) https://royalsocietypublishing.org/doi/10.1098/rspb.2019.2736

(6) https://www.pnas.org/content/113/21/5970

(7) https://www.nature.com/articles/s41396-017-0042-4

(8) https://deepcarbon.net/life-deep-earth-totals-15-23-billion-tonnes-carbon

(9) https://www.nature.com/articles/nm.4039

(10) https://www.tandfonline.com/doi/abs/10.3109/1040841X.2014.962478

(11) htt2s://www.researchgate.net/profile/David_Bhella/publication/305235846_Are3viruses_alive/links/5be0222b4585150b2b9faed8/Are-viruses-alive.pdf

(12) https://www.pnas.org/content/106/29/11827

(13) https://pubmed.ncbi.nlm.nih.gov/18690211/

(14) https://www.medecinesciences.org/en/articles/medsci/full_html/2018/13/msc180203/msc180203.html

(15) https://www.pnas.org/content/110/42/16736

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Acknowledgements
David Bikard, Jérémie Blache, Thomas Landrain, Mariam Chammat

* colorised by Marie-Sarah Adenis

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