Our microbial planet

Originally, 4.5 billion years ago, our planet was a lifeless sphere of molten metal. But after a billion years, the oceans were swarming with free living cells. Somehow, not yet entirely clear to science, life was born in these primeval seas. Some say that the first "bricks" of life flew dust from outer space – this is the so-called hypothesis of panspermia. Others believe that self-reproducing molecules appeared in clay deposits at the bottom of the ocean, in hot hydrothermal vents, or in foam bubbles that appeared when the waves crashed against the rocks. We still don't have an exact explanation of how it all began.

And yet, we more or less understand how, thanks to simple rules, the rich and diverse life of our planet has appeared and complex organisms continue to appear. All biology is based on the immutable principles of evolution, competition and cooperation that first emerged in the primeval oceans.

We live on a microbial planet that is completely dominated by life forms that are not visible to the naked eye. About 3 billion years bacteria were the only living inhabitants of the Earth. They lived everywhere on earth, in water and air, triggering chemical reactions, creating the biosphere and conditions for the evolution of multicellular life. They’ve created the oxygen we breathe, the soils we cultivate, the food webs for our oceans. Slowly, inexorably, through trial and error in the abyss of time, they have built complex and robust feedback systems that to this day sustain all life on Earth.

It is very difficult for a person to imagine this abyss of time, billions of years of activity of microbes that turned inorganic matter into living matter. This idea came from Geology – our understanding of how continents formed, drifted, diverged, crashed into each other, creating mountain ranges that were then eroded by wind and rain for millions of years. Nevertheless, bacteria lived on Earth long before the emergence of giant supercontinents of Laurasia and Gondwana, formed half a billion years ago; they are the ancestors of today’s continents.

John McPhee in one of his classic books gave a remarkable analogy with the place of mankind in this huge chronology: “let’s imagine that the whole history of mankind is one old English yard, equal to the distance from the nose of the king to the tip of his outstretched hand. It is worth a single time to hold the nail of the middle finger with a nail file, and you will erase all human history»

Or this. If we imagine 3.7 billion years of life on Earth as 24-hour days, our hominid ancestors would have appeared 47-96 seconds before midnight. Our own species, Homo sapiens, is 2 seconds before midnight.

But there’s also some amazing data that really makes it possible to assess how vast the microbial world is. They are not visible to the naked eye, with a few exceptions, only confirming the rule {12}. Millions can pass through the eye of one needle at a time. But if we put all of them together, not only will there be more than all of the mice, whales, people, birds, insects, worms and trees – all of the visible life forms on Earth – put together: they will be even heavier. Think about it. Invisible microbes make up most of The earth’s biomass: mammals, reptiles, marine life, etc.

Without microbes, we could not eat and breathe, but without us, almost all of them would live perfectly.

The term microbe refers to several types of organisms. This book talks mainly about the domain of bacteria, also called prokaryotes – single-cell nuclear-free organisms. But this does not mean that they are primitive. Bacterial cells are completely self-sufficient creatures: they can breathe, move, eat, get rid of secretions, defend against enemies and, most importantly, multiply. They come in a variety of shapes and sizes. There is like a ball, a carrot, a boomerang, a comma, snake, brick, even the tripod. Everyone is perfectly adapted to life in this world, including those who live in and on bodies. When they leave us, big problems begin.

Another microbial domain, archaea, at first glance resembles bacteria, but as the name itself says, it is a very old, deep branch of the tree of life with a different genetics, biochemistry and independent evolutionary history. They have been found in extreme environments, particularly hot springs and salt lakes, but in fact archaea can be found in many niches, including the human gut and navel.

The third branch of microbial life – eukaryotes, single-celled organisms with the nucleus and other organelles, which are the “building blocks” for the construction of more complex, multicellular life forms. Over the past 600 million years from eukaryotes occurred insects, fish, plants, amphibians, reptiles, birds, mammals – all “big” life, from ants to Sequoia. However, some of the primitive attribute to the microbes, including fungi, algae, some amoeba and slimy mold.

Here is another example that will help to estimate the scale. Everyone knows what family tree is. You place on it their ancestors-parents, grandparents, great-grandparents, etc., and their number is growing with each generation. Now imagine the family tree of all life on Earth – there are so many different forms of life that it looks more like a Bush with branches sticking out in all directions. Imagine for a second that this is a round Bush in which the first generation – the very first living organism – is in the center, and the branches stick out. Then we’ll put us people somewhere, say, for eight hours, if you look at the dial.

Now the question is. Where is the life form we call “corn” that grows in our fields? You probably think that it is unlikely to be too close to us, in the end it is a green plant. Probably somewhere on the other side of the Bush. And here and there, the corn is about at the point of 8:01. If people and corn are so close, as it turned out, relatives, who occupies the remaining branches? Answer: for the most part bacteria. For example, the distance between the two frequently occurring E. coli and Clostridium is much greater than between us and corn. Humanity is just a grain of sand in a world inhabited by microorganisms. You have to get used to the idea.

And then there are viruses, which are, strictly speaking, non-living; they spread, invading living cells and using their resources. Remember the flu, cold, herpes and HIV, which are considered a problem of humanity. But the majority in this world, in General we are not interested in: they infect bacterial cells and not animal, such as ours. Their number in ocean waters is incalculable: more than the stars in the Universe. In billions of years of fighting between viruses and microbes, both have developed weapons to kill each other. In fact, one of the possible ways to treat bacterial infections is to use phages, viruses that kill bacteria. I will touch upon this idea closer to the end of the book.

Our world is home to (and forms it) many different microbes, but let’s focus mostly on bacteria and what happens when we indiscriminately kill them with powerful drugs. There are, of course, a lot of eukaryotes (for example, Plasmodium falciparum, one of the main causative agents of malaria), causing severe suffering, but the problems that they deliver, of another kind. Viruses that cause great harm, too, enough-remember at least HIV – they are not treated with antibiotics. But this is a separate topic and a separate book.

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Germs live everywhere you look. There are so many in the ocean that it is impossible to imagine, although some estimates give some understanding. At least 20 million (and possibly a billion) types of microbes make up 50-90% of ocean biomass. The number of such cells in the water column (from the sea surface to the bottom) exceeds 1030, or nonillion (one thousand billion billion billion). They weigh as much as 240 billion African elephants.

The international census of ocean micro-organisms, a ten-year project that collected samples of marine microbes from 1,200 different locations, claims that different genera of micro-organisms are actually a hundred times larger than previously thought. In each studied place, some necessarily dominated both quantitatively and in activity. But, surprisingly, found a lot of those who are represented by populations of less than ten thousand individuals (for bacteria is a scanty number), including single specimens. Scientists have concluded that many rare bacteria have entered standby mode, preparing to bloom and dominate as soon as the environmental conditions are suitable. The same is true for the microbes that live in our bodies. The ability to” hide “by a few colonies over long periods and then spontaneously” blossom ” is an important aspect of their lives.

Many marine microbes are so-called extremophiles. They live in hydrothermal vents where boiling water, rich in sulfur, methane, and hydrogen, rises from the mantle and meets ice water, forming cone-shaped crevices. It’s a hell of a mixture of acids and heavy chemicals, but even under these conditions, without oxygen and sunlight, rich communities thrive. The same can be seen in the hot ponds and geysers of Yellowstone national Park in Wyoming and in the bubbling bitumen lake on the island of Trinidad in the Caribbean sea. Bacteria live in the huge glaciers of Antarctica, and in the icy depths of the Arctic ocean.

The ocean floor, made up of dark volcanic rock and 60% of the earth’s surface, is home to perhaps the largest population of microorganisms on the planet. They live off the energy produced by the reaction of rocks with water.

Recently, bacteria have been found that eat plastic particles floating in the oceans. This is a slow process, and yet at least a thousand different species are involved in the transformation of the “plastisphere” into a healthier biosphere. We didn’t do anything to encourage them – except throw plastic garbage in the ocean. Some got to it, and those who liked such food began to multiply faster – here’s a natural (plastic) selection in action.

In the deepest place on Earth, in the Mariana trench, recently discovered an active community of microorganisms, and there are ten times more bacteria than in sedimentary rocks surrounding the depression of the abyssal plain. Giant “carpets” – the size of Greece-live on the ocean floor off the West coast of South America, eating hydrogen sulfide.

Winds, including hurricanes, lift many microorganisms into the air; some survive and even remain there. Around are formed of ice particles, snowflakes, and there are Cirrus clouds. They influence weather and climate, process nutrients and decompose pollutants.

On the surface of the Earth microbes manage the soil-one of the most precious resources. Projects have been launched to collect soil bacteria in different parts of the world, some experts call it “the search for dark matter of the Earth” by analogy with the study of the nature of unexplored expanses of space.

They live in rocks. For example, in the gold mine of Mponeng in South Africa survive due to radioactive decay: uranium separates water molecules, and the resulting free hydrogen is combined with sulfate ions, getting food. Moreover, they even eat gold. Delftia acidovorans with the help of a special protein converts gold ions, poisonous to her, in an inert form, which is deposited from the surrounding water and forms mineral deposits. The most tenacious in the world of bacterium, Deinococcus radiodurans lives in radioactive waste.

We know that our planet is inhabited by microorganisms. They decompose dead matter-this is a very valuable service. In addition, inert nitrogen is converted from the atmosphere into free nitrogen, which can be used by living cells. And thus benefit plants and animals. After the oil leak in the Deep Water Horizon well in the Gulf of Mexico, the bacteria ate most of the contaminants because they managed to season the nutrients in the oil with nitrogen from the air, arranging a set lunch.

But my favorite example was described a few years ago. Geologists drilled a research well and studied the extracted cores. One, which got from a depth of a mile, consisted of only three components: basalt (native breed), water and bacteria – set of bacteria {16}. They lived and bred on a diet of stones and water.

Finally, entire industries are based on their work: making bread that we eat, alcoholic beverages that we drink, modern medicines developed by the biotechnology industry. It can be argued that microorganisms are able to carry out any necessary chemical process. In a huge variety lie unheard of opportunities. You just need to clearly identify the problem and find the bacteria that can solve it, or change them with genetic engineering.

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The history of microorganisms is a Saga of endless wars and cooperation. Since many are familiar with Darwinian ideas about competition and survival of the fittest species, let’s start from there.

Darwin’s careful observations have shown that individual members of the species are always different, take birds or humans as an example. The scientist developed the theory of evolution, putting forward the postulate that in the existence of different options nature “will select” the one (or those) who are the most adapted (“adapted”), who best used his cycle of life and left offspring. They win the competition with other species and will eventually begin to outperform them. Perhaps even cause the extinction of the latter. Natural selection is the reason often referred to as”survival of the fittest”. But Darwin didn’t know that the same principle could be attributed to microbes. Like us, he focused primarily on what he saw with his own eyes – plants and animals. But in fact, almost the best evidence of natural selection was obtained through observations and experiments on microorganisms.

For example, I can grow a culture of a common intestinal bacterium called E. coli by placing a few of the existing cells in a nutrient Cup. Overnight in a warm incubator, it can yield up to 10 billion new cells. The whole Cup will be covered with a carpet so dense that individual colonies can not be distinguished. And now suppose I did the same seeding in another Cup, but added streptomycin, the antibiotic that kills most of the E. coli strains. The next morning, I’ll see only a dozen isolated colonies the size of a miniature pimple, each with a million cells. Each cluster comes from a single one that survived contact with the antibiotic and then multiplied. How to explain the difference in results between sowing with and without streptomycin?

First, we see that the antibiotic worked. Instead of 10 billion cells only 10 million, that is a thousand times less. We can say that the antibiotic killed 99.9 % of cells, allowing only a small number to survive. But still, the drug didn’t work completely. Some managed to survive. So why did some cells survive and others didn’t? Just lucky? Yes and no.

Luck is that cells resistant to streptomycin have a variant of the gene required for the production of coli proteins, without which they can not exist. It is not very effective, but it is enough to help resistant strains survive and produce offspring. The rest die because the antibiotic interferes with the normal version of the same protein.

The genetic variants that provide this property appear in an interesting way. It is possible that some cells (in this example – ten) from the original culture in a billion had a similar variant of the gene. These cells existed originally. Describing the experiment in Darwinian terms, we can say that streptomycin ” selects “in the population variants with a resistant form of the gene, but the absence of an antibiotic in the environment” selects ” more effective, but vulnerable to it the usual form. Number Of E. coli with this property depends on how often and how long they have been in contact with streptomycin. It’s a simple example of natural selection, but the competition is eternal. Let the strongest microbe win.

Some compete with others, prey on them and even exploit them, but there are countless examples of cooperation and synergy. For example, if the intestinal bacterium Bacteroides can purify a chemical substance in the environment that interferes with the development of E. coli, then it is beneficial to the second. Unilateral beneficial relationship of this kind is called commensalism.

Interaction is even stronger if it is beneficial to both sides. Imagine that the coli serve as a good source of food for the Bacteroides. In this case, these two species will be collected in the same environment. Both just follow their own program, but help each other. It’s symbiosis.

In other conditions creating symbiosis with other bacteria. For example, in a fast stream, bacterium a eats bacteria b excretions, and also adheres to the sharp edges of the stones. Bacteria can not stick to, but can cling to the bacterium A. Bacterium b produces a substance, a nutrient for B. Here is a situation where bacteria a, b and b will meet together, and to the benefit of all three.

For more than 4 billion years of bacterial evolution, given that some are divided every twelve minutes, as well as their astronomical number, the options were almost infinite. Thanks to this constant process, there were some bacteria that inhabited all available niches on Earth.

Sometimes they live together stably, forming a consortium. Such cooperative groups are found in abundance in the environment – in soil, streams, rotting logs, hot springs-almost everywhere where there is life. The oldest unequivocal proof of the existence of life is a fossilized bacterial mats age of 3.5 billion years, found in Australia. Consortiums, consisting of huge sheets lying on each other, are full-fledged miniature ecosystems. Most likely, some were engaged in photosynthesis, others breathed oxygen, the third carried out fermentation, the fourth ate unusual inorganic compounds. The fact that one species is the food, another’s poison. By gathering in layers and joining forces, they were able to ensure survival for all.

There are microorganisms that are able to create around themselves layers of a substance similar to gelatin. This dense gel is called biofilm. The composition is different, but it protects the bacterium from drying out, excessive heat, attack the immune system. Its existence explains the presence of bacteria in the most severe conditions.

Microbes form consortia and vast networks of cooperation not only in soil, ocean or rocky surfaces, but also in animals. In the human body, these are the main characters in my story about”missing microbes.” The great biologist Stephen J. Gould gave us a starting point for all of earth’s biology by writing:

We live in an era of bacteria (as it was in the beginning, as it is now and as it should always be, until the world comes to an end…)

This is the context of human life-its foreground and background.