Some organisms never quite worked out how to live with it. This is the story of where they went.

Off the coast of Japan, for four months a year, the deep blue sea is transformed into a stunning galactic landscape. Minuscule blue lights dance and sparkle, lighting up miles of coastline. Thousands of creatures that might be stylistically drawn works of pointillism cling to the beach. From afar, it looks like an electric blue Aurora Borealis has bled into the water.

How does this happen? Meet the hotaru ika.

The firefly squid, or Watasenia scintillans, is a small creature no more than three inches long. In Japan, it is known as the hotaru ika. Although resembling a lightning bug, the firefly squid has over a dozen lights that litter its body, instead of just the one. More notably, it is usually can’t flash them on and off in a regular pattern. That means the lights likely don’t serve any of the more obvious purposes, like attracting mates or scaring away predators.

So, why do they glow at all?

One emerging theory is oxygen.

About 2.4 billion years ago, the bacteria of Planet Earth began fighting the first great battle of their lives. The enemy in this case was no mortal creature, but a toxic chemical gas that was spreading into every corner of the world. And its name was: Oxygen.

In the early days of the Earth, when life first began, there was no oxygen. Not much to speak of, anyway. It was all trapped away in the rocks and soil, or floating in the air as harmless carbon-dioxide. That’s why bacteria were never adapted to deal with it. To them, oxygen was a toxic poison.

Then, some bacteria started to photosynthesise. They began to capture the energy of the Sun, to help themselves grow and live and spread. These energy-harvesting bacteria were very successful, and began to spread everywhere. But their energy-harvesting had a side-effect: the carbon-dioxide broke up, leaving some of its atoms free to form oxygen.

At first, that was quite okay. The oxygen would get absorbed into the rocks, or taken up by the ocean water. But then, then the rocks and oceans began to get saturated. They were so full-up that they couldn’t take any more. The oxygen began to escape into the atmosphere.

At that time, no creatures knew how to do anything with oxygen. They couldn’t breathe it or absorb it – or, really, do anything at all with it. So the oxygen began to build up, in what is known as the Great Oxidation Event, reaching levels even greater than those of today.

Some creatures adapted to this increase. They just had to get rid of the oxygen somehow — and one of those ways was to burn it off by making a glowing light. This, then, could be how fireflies and hotaru ika evolved. That the lights could be used in other ways was just a helpful side-effect.

Some animals did better. They actually took advantage of the oxygen, and used its powers to build up on their own. But others never worked out how to live with oxygen. They had to flee, to the nooks and crannies of the planet.

Buried beneath an entirely unremarkable field, the Moville Cave seems like it might be as far removed from the rest of the planet as the moon. In fact, the number of lunar explorers is comparable to the number of people who have entered the cave.

Sealed for five million years, the toxic air and humid conditions gave rise to a plethora of otherworldly creatures. Most are unpigmented, with colourless skin. They have spindly limbs and antennae to help navigate in the darkness. And, perhaps most importantly, the entire system survives not on photosynthesis — there is no light in the cave — but by the energy released in other chemical reactions that are then harnessed by the bacteria.

Isolated ecosystems exist all over the world. Many islands, such as the Galapagos range, are examples of ecosystems that have evolved independently of outside influences. But the Galapagos still have exposure to the outside air. Some places, like sealed caves or underwater vents, don’t have even that.

And these are the places where our friends, the oxygen-shy bacteria, took refuge.

As the oxygen spread, these ancient bacteria were pushed back to areas that had little to no contact with free oxygen. For them, these places were perfect habitats, as they were also allowed to become part of a greater community of creatures.

Bacteria also sought asylum in another place — one that is, perhaps, closer to home for you and me.

They hid in other creatures.

Animals, including humans, are filled with bacteria. They aid with digestion in the gut, breaking down food that we’d never be able to handle ourselves. They supply us with nutrients like Vitamin K, and help develop our immune systems — and do many other things besides.

In fact, there are about ten times as many bacterial cells in our bodies as there are human cell, so we could already be considered more bacteria than human. And if all the bacteria in your body were wiped out — say by a new super-antibiotic — you would probably die.

Turns out, we’re managing to do the job just fine even without the super-antibiotic.

In 2009, a group of scientists visited the Yamomami tribe of South America, to study their stomachs. More specifically, they wanted to see what kinds of bacteria lived in those peoples’ digestive systems, and how they compared to “modern” humans living back in the U.S. The results were surprising.

While the researchers expected to find different kinds of bacteria living in different stomachs, they thought the number of different kinds would be roughly the same. As it turned out, Yamamoto stomachs had one-and-a-half times as many species as the average Americans did. And it’s not just Yamamoto—as further studies have shown, “tribal” societies consistently have more bacteria in their bodies than “modern” ones.

How is this possible?

One explanation is diet. The Yamamoto had no concept of mealtimes: they just ate when they were hungry, and ate several times a day. So that could have had an impact on the diversity of critters in their gut.

But there’s also a more powerful explanation: these bacteria-rich indigenous people had never before been exposed to antibiotics.

Antibiotics are poisons for bacteria. If you fall sick with a bacterial infection, you can take antibiotics to kill them off. But antibiotics aren’t very specific, so they kill a lot of good bacteria too. That’s why, if you take antibiotics, your digestive system gets thrown out of order for a while.

But what if those good bacteria don’t come back? They have to come from somewhere, after all. If they can travel through the air or food, all’s well and good — but there could be some bacteria that get passed on from mother to child, and never travel after that at all. The situation’s so bad that some Americans even do “faecal transplants”, where they actually import digestion-helping bacteria from one person’s gut to another’s.

But is it just about antibiotics? Not quite.

Another group of scientists studied the stomach bacteria of Papua New Guinea. The Papua New Guineans had more stomach microbes than Americans too — even though they had been using antibiotics for quite a while.

The new group thinks it’s not just antibiotics that are to blame. It’s the general idea of “hygiene”. In societies like America, people wash their hands often. They like to use soap and shampoo and disinfectants; they like to keep things clean. That’s been very effective to stop bacterial disease from spreading — but the flip side is, it stops bacterial helpers from spreading as well.

People whose cultures creep closer to the Western don’t just misplace gut bacteria species. They start to lose the potency of their immune systems.

Aside from helping us break down food, bacteria also help keep us safe from diseases. When disease-causing bacteria enter our systems, they’re posing as competition for the ones who are already in there. It’s in the best interest of these bacteria to wipe out the invaders. This is how they keep their own numbers constant.

It’s the bacterias’ way of protecting their own unique species: painstakingly cultivated, highly specialised, and unable to survive out there in the toxic, oxygen filled air.

That they keep us from dying is only a side effect.

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