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Section: Biology
Microbes: Keeping it Going

Microbes: Keeping it Going

In the study of nature, reductionism seeking out to explain the whole by considering its parts alternates with the system approach attempting to do the reverse. The former has now developed into the dominating ideology Darwinism with molecular genetics as its weapon of choice; the latter into geobiospheric attitudes expected to answer the question as to whether a sustainable development is at all possible

Looking rather like a pyramid,

evolution is traditionally portrayed as a tree,

which is referred to accordingly — an evolutionary tree.


Before we go about using the concept of life, let us see first that we have the right idea about the concept of a system. So what is it all about? First, any system consists of interdependent parts. For instance, the simplest unicellular organism consists of the following four parts: a membrane, which delimits the cellular environment from the surrounding medium, genetic material in the form of DNA, a ribosome (a protein synthesis apparatus), and the cytoplasm, that is the cell’s internal environment suitable for metabolism.

Secondly, and this is the main point, the properties of a system are not just a sum of the properties of its component parts. This is where a new quality arises. For instance, consider again the original discreteness of life: although all of the cell components perform specific biological functions, life is the property of a system of the components combined into a single organism, and so is known to us.

The next important point is that any system is hierarchic. To study a system correctly, a three-level analysis is required. That is, it is required not only to consider all the parts of the system, but also to work out what the major system that incorporates it is like. Likewise, any organism does not exist all on its own but as a component part of an ecosystem, which includes its habitat. The multiplicities of ecosystems, in turn, are component parts of the biosphere, which includes the terrestrial biota and geospheric shell. And this major system is critical for the existence of life.

There are two more very important properties of systems, which we shall turn to later. First, to be entitled to a system, the function(s) of a candidate entry should be adequate to it. Second, the system’s functional components can be replaced by other components provided the latter have similar functions.

Lest it be thought I am wasting time on the fundamentals of the system’s analysis, try and predict the properties of the biosphere by looking at the properties of the informational genetic molecules! That would be as silly as searching for a ‘universal common ancestor’ without a good knowledge of the habitat and geochemical processes it should be adequate to in order to linger on in this world. In order to understand how life emerged and started out, one should reason in terms of analysis of large systems, on a top-down basis, from particular to general, which is exactly how we will try to treat the evolution of microbial communities.


First of all, Earth’s early biosphere was created by bacteria or, to put it more precisely, prokaryotes, i.e., unicellular organisms lacking a nucleus. Because, except for single occurrences of metamorphed Archaean rocks, we have no geological evidence to be sure of what the prokaryotic biosphere was like in the period preceding to 3.5 billion years ago. That is why modern reconstructions are only based on analogy and therefore are somewhat unreliable.

At the dawn of life on Earth, only a prokaryotic community existed and the whole biosphere was created by bacteria. Any later event could only be a modification made to the system that had been crafted by those invisible things when they were given full reign

All free-living organisms are fueled by redox reactions. The most primitive microbial community is the one of hydrogenotrophic microorganisms. The reducing agent they use is hydrogen, which is produced by water reacting with overheated rock, that is at quite high temperatures. Such organisms occur widely among the microflora living in rock pores at depths exceeding 3 km. Thus, these relic forms can have been living safely, with no risk of exposure to UV radiation, which would have been perilous, as there was no ozone layer to protect them.

Unfortunately, these microorganisms still include photoautotrophs that have become the main producers of organic matter on Earth. They were the first to make use of sunlight as a novel external source of energy on our cooling planet. The photoautotrophs turn to action at temperatures ranging from 0°С to about 60°С.


Cyanobacteria, also known as blue-green algae, are some of the most significant photoautotrophs. These amazing self-supporting organisms, mistakenly referred to as algae, can be found anywhere, be it a rain forest, a mountain, a sea, or a nuclear testing ground. Like algae and plants, they have the pigment chlorophyll needed for photosynthesis.

Since cyanobacteria came to existence, our biotic system has become self-supporting, with self-contained cycles of all biogenic elements. Cyanobacteria are the primary producers of organic matter and free oxygen in the atmosphere, haemotrophic bacteria are consumers that destroy organic matter and bring it back to the biotic cycle. Incomplete destruction leads to accumulation of carbon by sediments. Sedimentary rock carbon is referred to as kerogen.

Based on paleontological data, the earliest cyanobacteria, whose structure is similar to that of the existing ones, lived 2.7 byr ago. It is interesting to note that these unthinkably ancient organisms are readily identifiable by using modern reference books — billions of years of existence have caused very little change in them! Admittedly, this figure is arbitrary, because, for example, the small coccoid blue-green ones inhabiting the ocean, are barely discernible under a microscope. That is why although organisms like these may have existed long before that, their traces may escape modern detection techniques used in bacterial paleontology.

The blue-green algae found in the ancient rocks on land are 2.2 byr. Also, they may have lived in wet soils, ephemeral water bodies and porous rocks (like those occurring in modern deserts and the Antarctic), in which their fossils did not survive the test of time. Stromatolites — bizarre ‘stone carpets’ made of stoned fecal specimens left by ancient cyanobacterial communities, both producers and consumers — are the memories of ancient blue-green algae.

These communities created a perfect biosphere of the modern geochemical type. It existed for 2—3 byr and gave rise to sustainable life. If the population and viability of the organisms were to be considered as a criterion for evolutionary advancement, then the cyanobacterial community would win hands down.


The next step in the evolution of our system is associated with the emergence of eukaryotes (organisms with a perfect cell nucleus) and multicellular organisms. Although it is not known when exactly they emerged, one thing is for sure: the eukaryotes did not play the main role before 1 byr ago.

The evolution of living organisms is normally rendered as a genealogical tree originating from few ancestral forms, which supposedly dropped out later on as the least fit. In fact, the representatives of all main groups of organisms — from the most to the least primitive — that has ever emerged coexist

Note that the eukaryotic and multicellular organisms did not emerge in the middle of nowhere but in the prokaryotic biosphere as their habitat. The eukaryotic biota was much ‘narrower’ than the prokaryotic biosphere: only bacterial organisms could withstand the harsh environmental conditions: high temperatures, high salinities, etc. Such relic microbial communities that still live in highly saline lakes, sea lagoons, and hydrotherms may serve as models of the ancient biosphere.

Hence a considerable shrinkage of the base of life. As the system approach demands, the new may not defy the old, and the preservation of the old is a necessary condition for a sustainable development of the system, i.e., evolution. Thus conceived, evolution ceases to look like a tree and appears as a pyramid (or, if the reader is so inclined, the Tower of Babel).

AN «ALTERNATIVE» LIFE Extensive fields of giant bivalves, thick shoals of shrimps and clusters of vestimentifera tubeworms as if an alive spaghetti plant found deep in the ocean near the Galapagos Islands by a joint French-American expedition in 1977 was the most fantastic discovery of the time. The scientific world was struck as nobody could expect to see oases of exuberant life in kilometers-deep water, in the dark, under enormous pressure. Now they are known in all oceans at depths from 400 to 7,000 m.
Burning-hot 1,200°С lava rising through fissures from the mantle to the surface in oceanic rifts meets sea water leaking down. The water heats up to 500—850°С, uptakes sulfur and metal compounds, and springs in hydrothermal vents called ‘black smokers’ (because of dark iron sulfide suspension).
Communities that live in the vicinity of hydrotherms in the absence of light utilize the chemical energy from chemosynthetic sulfur bacteria. These bacteria produce organic molecules obtaining energy by oxidizing sulfur compounds and are the base of the vent community food chain. The body of Vestimentifera Riftia tubeworms, which grow more than 10 feet long tubes with bright-red gill tentacles put out therefrom, almost entirely consists of a large spongy organ called a trophosome that hosts up to 10 million chemosynthetic bacteria inside. Tubemakers and bivalves, eaten by shrimps, crabs, and fishes, likewise live in symbiosis with these bacteria: they live on the body surface of Alvinella tubemakers and bivalves have them living in their gills. Areas around black smokers are home for about 500 species known by now in vent communities.
Lev Zonenshain, Russian geologist, one of the first who brought in plate-tectonic views, wrote in 1979 that the Urals possibly had formed in place of a closed ocean, and the pyrite deposits in the Southern Urals sourced from fossil Silurian-Devonian ‘black smokers’. Russian scientists did find typically hydrothermal fossil biota there later. Then the discovery of still earlier Precambrian ‘smokers’ followed. Thus the question arose whether life can have begun in these ‘sulfur pots’? Sulfur compounds remain energy sources for cells, not only in vent-community organisms. Can it be a due to the remote past when the life ‘seeds’ grew near hot sulfur vents?
A community of organisms living in the vicinity of a hydrothermal vent was discovered in the 1980s in Lake Baikal in diving experiments with “Pisces” manned submersibles. The vent erupting highly mineralized thermal water is located in the Frolikha Bay, North Baikal, at a depth of over 400 m.
The Frolikha vent is surrounded by ‘glades’ (mats) covered with white filamentous films of cyanobacteria and filiform sulfate-reducing Thyoploca bacteria, thick colonies of sponges, abundant worms, molluscs, crustaceans, and fishes. Note that the community includes many large species, though the deepwater fauna of Baikal mostly consists of small animals.
The blue color of sediments near the vent is evidence of an anoxic near-bottom environment, which is however overwhelmingly inhabited. The biota of the Frolikha vent is equivalent to ocean-bottom communities in relatively cold methane-sulfate seeps. The Baikal vent community likewise lives mostly on methane produced by chemosynthetic bacteria.
The hydrothermal oasis of a wonderful ‘alternative’ life in Baikal is another exceptional feature of this little freshwater ocean.


Things able to fulfill the same functions as prokaryotes emerged in a new, prokaryotic world, which appeared as an add-on to the prokaryotic biosphere. First of all, they were algae, which like cyanobacteria, were capable of photosynthesis. They began to explore the ocean and withdraw cyanobacterial communities from shallow seas and lakes. However, unlike the blue-green algae, the true algae are not capable of atmospheric nitrogen fixation, which is a serious disadvantage.

Relic microbial communities, living in the harsh environmental conditions (for instance, in hydrotherms or soda lakes), are analogs of past ecosystems. That such communities live where no other does implies that the evolution and growth in the complexity of the organisms was accompanied by a shrinkage of the base of life

The biosphere solved this problem at a community level: excessive synthesis of nitrogen-free organic matter by eukaryotes gave rise to nitrogen-fixing bacteria that consume organic matter. This example illustrates that the main character in nature is not a separate organism or species, but a community as a cooperative unity.

Thus, in any community priority is given to trophic, i.e., food chains which trigger ‘matter turnover’ in a manner of cell metabolism. All the groups of organisms in a community are responsible for keeping complementary chemical reactions running; and what is more, any organism can be replaced by another, no matter of what origin or species, provided it performs the same function. The individual does not matter, the community does! And the community as a whole is restricted by the requirements of the geophysical environment, first of all — the requirement of element-to-element matter transport. Only a unified enclosed system of functionally complementary organisms can meet these requirements. There is no such a thing in the real world as a universal soldier able to complete any mission.


The bacterial world was considerably handicapped in that the structure of prokaryotes was incompatible with the ability to consume solid matter. Passage of a solid particle through the membrane would disrupt the cell’s functioning. That is why the prokaryotes never became predators. Changes in the membrane structures of the earliest simplest unicellular eukaryotes, which enabled them to capture solid particles, were by far the most revolutionary improvement preceding any other changes in the architecture of their cells. From then on, cell envelopes could be digested within organisms, and so bacteria became a prey. Before that milestone was reached, prokaryotes would die out due to their internal reasons, but after that the rules changed: gone hunting were the first bacteria-lusted predators...

As the evolution of the communities was going on, every step towards higher complexity in the organization of living creatures was accompanied by the emergence of new niches for bacteria. Because the digestive tract is exactly the way it is, to gut organisms, the animals are but walking tubular fermenters. Whatever further growth of complexity food chains are up to, one rule remains the same: the primary organic matter producers — the cyanobacterial-algal-floral link — go first and the consumers go last. At no point shall the life circle be broken.


And what can we see if we look down from the top of progressive morphological evolution? The geosphere was changing, and so was the biota, subordinate to it. New organisms would emerge, evolve and vanish; however, the microbes have always been the backbone to the Earth’s life support system. That is why our huge geobiospheric machine, which consists of interconnected geobiochemical cycles and processes, which are linked by global matter and energy turnover, has always been up and running.

A microbial community does not emerge through divergence, speciation, or acquisition of unique features by species, but is compiled from phylogenetically distant, ‘unrelated’ organisms favored by the landscape. In this sense, the evolution of microbial communities — the ultimate driving force of the evolution of the biosphere — seems to have nothing to do with that as per Darwin

What is the price of evolutionary progress? Morphologically advanced as we eukaryotes are, we only account for as little as 3 % of carbon turnover! That is a pittance compared to the load that the microbes have to carry! However, we do not bother to think about them until we catch a cold, our milk turns sour or our favorite swimming pool gets overgrown. I, for one, do not seem to recall Greenpeace campaigning over an endangered rare species of little cyanobacterial champions. On the other hand… What need do the true champions have for our support, approval or whatever?

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