MICROBIOLOGY: THE BIOLOGY OF PROKARYOTES, VOL. I - A. V. PINEVICH - 2006

CHAPTER 6. CORE PROPERTIES AND SIGNIFICANCE OF PROKARYOTES

Class="center">Small is not only beautiful — considering the elegance that microbes permit in PHYSIOLOGICAL AND BIOCHEMICAL experiments — but also intrinsically powerful.

(Small entities are not only beautiful, judging by the elegance of microbes in physiological and biochemical experiments, but also possess inherent power).

H. G. Jannasch. Small is powerful: recollections of a microbiologist and oceanographer (Ann. Rev. Microbiol., vol. 51, 1997).

The Biological Significance of living organisms is evaluated through the lens of criteria such as geographical distribution and habitat; ecological niche; reproduction rate and total population size; morphophysiological and behavioral adaptation (the reaction norm of the genotype); intraspecific and interspecific relationships; and The Nature of environmental impact.

The biological significance of living organisms depends on their Structural and functional properties, primarily on their type of Cellular Organization. Bacteria and archaea belong to the prokaryotic morphotype, meaning they are "anucleate Cells". The prokaryotic morphotype, in turn, is represented by several variants (see Chapter 8).

6.1. Key Properties of Prokaryotes Compared to Eukaryotes

Dichotomous mega-Classification is based on a comparison between PROKARYOTES AND EUKARYOTES. For this comparison to be valid, METABOLISM/2.html">THE CONCEPT OF a "eukaryote Cell" must be distinguished from that of a "nucleate cell".

Eukaryote cells are monads belonging to the phylogenetic domain Eucarya.

Most nucleate cells are chimeras. Constantly overlooking this fact, people refer to nucleate dyads (cells with Mitochondria) or triads (cells with Mitochondria and Plastids) as "eukaryotes" rather than true eukaryote monads. However, a whole cannot be compared to its individual part.

Cells containing symbiotic Organelles do not possess an independent morphotype; rather, they represent a chimeric combination of two morphotypes — eukaryotic and prokaryotic.

From this follows a paradoxical Conclusion — chimeric cells (namely, the cells of protists, Fungi, animals, and plants) have no place on the universal tree of life.

6.1.1. Comparison Algorithm

One can compare prokaryotic monads among themselves — bacteria, archaea, mitochondria, and simple plastids. One can also compare eukaryote monads, i.e., nucleate cells lacking symbiotic organelles. Finally, one can compare a prokaryotic monad, such as a mitochondrion or a "simple" plastid, with its eukaryote host (in this case, comparing parts of a chimeric intercellular association rather than independent organisms).

Eukaryotes are represented by two variants of monads. In one case, the monad is not an independent Organism, but a host monad within a chimera (a dyad or triad). In the other case, it is an independent monad organism. Such organisms are termed "primary amitochondriate" protists and are descendants of eukaryotes that initially lacked mitochondria.

Do such organisms exist in the modern biosphere?

During the 1970s and 1980s, primary amitochondriate protists were thought to form a collective group called Archezoa. This group included members of the classes Archamoebae (e.g., Pelomyxa palustris), Metamonada (e.g., Giardia lamblia), Microsporidia (e.g., Encephalitozoon cuniculi), and Parabasalia (e.g., Trichomonas vaginalis).

In the late 1990s, it was discovered that the genomes of certain primary amitochondriate protists contain homologues of Mitochondrial Genes — such as heat Shock protein genes (Hsp10, Hsp70, and cpn60), as well as genes for Key Enzymes like adenylate kinase, pyridine nucleotide transhydrogenase, Triosephosphate isomerase, valyl-tRNA synthetase, etc. Their presence in the nuclear genome is attributed to "horizontal" Gene transfer from the mitochondrion to The Nucleus before these chimeric cells secondarily lost those organelles, i.e., when the protists transitioned from primary mitochondrial to amitochondriate states.

However, data on Homology with mitochondrial genes is not yet a decisive argument in favor of the mitochondrial origin of nuclear genes. After all, these might not be mitochondrial genes, but rather genes from symbiotic bacteria that temporarily took up residence in a primary amitochondriate eukaryote cell. Before these unsuccessful symbionts abandoned their host, some of their genes could have "migrated" into the nucleus, for instance, via a viral vector.

Although THE ORIGIN OF primary amitochondriate protists remains an open question, we are justified in considering them true eukaryotes, just as we consider true eukaryotes those nuclear hosts that form an integral part of chimeric cell associations.

6.1.2. Summary of Comparison

Taking these clarifications into account, we can compile a comparative table of the key properties of monads belonging to the phylogenetic domains Bacteria, Archaea, and Eucarya (Table 1).

Complexity of prokaryotes. Structurally and functionally, prokaryotes differ fundamentally from eukaryotes. Their organelles are multifunctional, and their energy and Intermediary Metabolism exhibits high lability. This represents a distinct type of complexity and a more streamlined type of cellular organization, free from an Abundance of secondary morphological details. Prokaryotes are not simpler than eukaryotes; they are simply "different".

Functional superiority of prokaryotes. When comparing leading genetic, cytological, metabolic, and behavioral traits, we find that prokaryotes surpass nucleate monads in their functional capabilities.

First, prokaryotes possess more diverse metabolic properties. Representatives of this morphotype are capable of phototrophy, respiratory chemotrophy, carbon autotrophy, and diazotrophy. At the same time, nuclear monads lack the genes encoding Proteins involved in these fundamental metabolic processes (with carbon autotrophy in the methylotrophic Yeasts Hansenula polymorpha and Pichia pastoris being a rare exception).

Second, prokaryotes exhibit greater diversity at THE MOLECULAR LEVEL. For instance, they feature structures formed by non-unitary membranes. The cells of most bacteria are enclosed in a rigid sacculus, or a bag-shaped murein molecule. Many bacteria also form resting, resistant cells known as endospores. Thus, prokaryotes possess structural and functional traits that are entirely absent in nuclear monads.

It should be noted that although identical terms (such as "chromosome", "trichome", "flagellum", "spore", "glycocalyx", "budding", "fission", etc.) are used in relation to both prokaryotes and eukaryotes, they denote heterologous structures or contrastingly structured processes.

Prokaryotes—including those that form a unique quasi-multicellular Structure, the trichome—function as organism-cells. Therefore, they can be roughly compared to amitochondrial protists, in which genetic, metabolic, transport, and regulatory processes are similarly restricted to THE CELLULAR LEVEL of organization. However, in prokaryotes, structures are polyfunctional, whereas Functions are less compartmentalized.

Diversity of metabolic types in prokaryotes. A crucial property of prokaryotes is The Diversity of their metabolic systems, which enable them to utilize various Energy Sources and structural substrates, including inorganic ones (Table 1).

Table 1. Comparative Properties of the domains Bacteria, Archaea, and Eucarya

Notes: (+) — property present; (-) — property not detected.

Bacteria possess 11 types of transmembrane Electrochemical Potential (Pmf) generators, whereas archaea possess 7, while eukaryotes energize their membrane structures solely via the Hydrolysis of ATP or inorganic pyrophosphate (PPi). Autotrophic Bioenergetics—namely, the assimilation of Free energy from light quanta with an energy of 1.5–3.5 eV (phototrophy), as well as the assimilation of energy released during The oxidation of inorganic substrates (lithotrophy)—occurs exclusively in prokaryotes. Respiration utilizing inorganic and organic electron Donors is likewise found solely among prokaryotes.

Autotrophic constructive metabolism, primarily the assimilation of inorganic carbon compounds, is widespread in prokaryotes and absent in eukaryotes. In turn, a great many bacteria and several species of methanogenic archaea possess the capacity for diazotrophy, or the assimilation of molecular nitrogen. This invaluable physiological trait is entirely lacking in eukaryotes.

Strategies of cellular evolution. The prokaryotic strategy consists of combining multiple metabolic pathways with the multifunctionality of cellular structures.

At the same time, the strategies of nuclear organisms include:

— increasing the degree of cellular compartmentalization (in the case of Protists);

— increasing the osmotrophic surface area (in the case of Fungi);

— diversifying mechanisms of transport, Nutrition, and long-range Regulation at the level of multicellular systems (in the case of Animalia and Plantae).

At an early stage in the evolution of organic life, eukaryotes acted as hosts in a chimeric cellular association. Their "junior" partners were bacteria, which evolved into semi-autonomous cytoplasmic organelles—mitochondria and plastids. The functional contributions of these bacteria to the chimeric cellular system included phototrophy, aerobic respiration, and carbon autotrophy. As a result, The rate of nuclear Cell Evolution accelerated, allowing them to colonize diverse niches and achieve dominance within THE SPECTRUM OF species diversity.

6.2. Significance of Prokaryotes

The impact of pathogenic bacteria on humans is a "sensitive" subject, and understandably so. Pathogenic bacteria affecting animals and plants are also viewed through the lens of anthropocentrism, albeit without undue dramatization. The colossal destructive impact of bacteria on the material assets of civilization is perceived as a "lesser evil." Conversely, the practical benefits they provide are often underestimated.

Setting aside human ailments and the problems of human civilization, the true biological significance of prokaryotes is determined by:

— their diversity spectrum, as well as total abundance and biomass;

— their role in shaping the planet's biogeochemical system;

— their pivotal involvement in the evolution of organic life.

In the second half of the 19th century, the founders of Microbial Ecology, Sergei Winogradsky and Louis Pasteur, concluded that the true significance of bacteria lies in their role in global natural processes. To reinforce this point in an 1896 lecture dedicated to the biogeochemical significance of bacteria, Winogradsky quoted Pasteur: "... le rôle des infiniment petits m’apparaissait infiniment grand" (French for "...The Role of the infinitely small appeared to me infinitely great").

Prokaryotes as "half" of living matter and as a reservoir of biogenic elements. According to current estimates, the total abundance of prokaryotes at any given moment is three orders of magnitude higher than the number of nuclear cells, reaching an astronomical figure of 5 • 10³⁰. This superpopulation is constantly multiplying. In the World Ocean alone, 2 • 10³⁰ cells are generated annually.

Although an individual Prokaryotic Cell is invisible to the naked eye (having an average volume of 2.5 µm³ and a mass of 10^-12 g), collectively prokaryotes account for a very substantial fraction of global biomass. It is estimated at approximately 5 • 10¹¹ tons (in terms of carbon), which equals the biomass of all nuclear cells combined. Albert Kluyver and Cornelis van Niel, in their joint lecture course The Microbe’s Contribution to Biology delivered in 1956, noted that half of the living matter on Earth is represented by bacteria.

The total nitrogen content in prokaryotic biomass reaches 1.3 • 10¹¹ t, and phosphorus 1.4 • 10¹⁰ t. This is an order of magnitude higher than in all plants combined.

Prokaryotes as the first living organisms, pioneers, and cosmopolites. Some of the earliest products of biological evolution were archaic Representatives of the phylum Cyanobacteria. The age of the oldest oxidized rocks, 3.5 billion years, corresponds to the age of microfossils (see Section 1.8), which strongly resemble modern cyanobacteria in appearance.

Cyanobacteria possess an exceptionally high adaptive potential, allowing them to thrive across a wide range of abiotic environmental factors and even colonize extreme niches. Specifically, troglodytic forms (derived from the Greek trogle, meaning cave, and phyton, plant) inhabit caves and grottos; Spirulina sp. strains cause Water blooms in soda lakes at pH >11; cyanobacteria colonies can be found in deserts and perennial snows; and under laboratory conditions, they are capable of growing in atmospheres of pure oxygen or carbon dioxide.

Cyanobacteria colonize the sterile surfaces of newly formed volcanic islands and "nuclear" atolls. They behave as autonomous cosmopolites capable of effectively developing in stressful conditions where no other bacteria are present, and of outcompeting others for energy or substrates in environments favorable to non-extremophilic microbiota. Although they grow rather slowly and are generally incapable of heterotrophy, they can always be found in the vicinity of more dynamic consumers. Low selective pressure has allowed cyanobacteria to preserve the essential structural and functional traits of their archetype.

The existence of prokaryotes is limited solely by the Physical and Chemical conditions that prevent the degradation of NUCLEOTIDES and Amino Acids. For instance, temperatures around 125°C mark the upper limit for organic life. Furthermore, prokaryotic development requires water in a liquid state; and while the atmospheric ocean could theoretically serve as the largest niche for colonization, it acts merely as a conduit for their dispersal.

As previously mentioned, prokaryotes inhabit aquatic environments, soil, and the Earth's crust. They develop as endoliths in rocky formations, form biofilms on solid substrates, live on plant leaves, as well as on the outer integuments and digestive tracts of animals. For endocytobiotic prokaryotes, the compartments of nucleated cells serve as a permanent niche. Pathogenic and saprophytic bacteria can colonize living organisms, necromass, and the post-mortem degradation material of animals and plants.

The majority of prokaryotes occupy poorly explored niches on the ocean floor and in the upper layer of the Earth's crust down to a depth of about 4 km. Further penetration into the Earth's crust is limited by the maximum tolerable Temperature, which rises on average by 3°C every 100 m.

Thus, prokaryotes populate all permissive (i.e., allowing vital activity) abiotic and biological niches.

In an anabiotic state, particularly in the form of endospores, prokaryotes are capable of bridging gigantic spatiotemporal intervals. They interact with nucleated organisms, including at the intracellular level, exerting structural, physiological, and regulatory effects upon them.

The cosmopolitan nature of prokaryotes and their ability to colonize diverse, often extreme niches are ensured by a broad norm of reaction of the genotype, along with genome plasticity and polymorphism. At the ecosystem level, this is manifested in a wide spectrum of coexisting life forms.

Prokaryotes and the symbiogenetic scenario of cell evolution. According to modern concepts, mitochondria and plastids did not originate via autogenesis, or the endogenous compartmentalization of The Eukaryotic Cell, but rather through xenogenesis, when bacteria colonized a eukaryotic host. Having lost their genetic, structural, physiological, and regulatory autonomy, they transformed into cytoplasmic organelles. Carl Woese coined the apt comparison that mitochondria are "domesticated purple bacteria," while plastids are "domesticated cyanobacteria."

Bacterial symbionts endowed nucleated cells with the capacity for aerobic respiration and oxygenic Photosynthesis, which constituted The most significant aromorphosis in the entire history of organic life.

The further Progressive development of chimeras led to the emergence not only of numerous protist groups, but also of the crown of the evolutionary tree represented by the kingdoms Fungi, Plantae, and Animalia.

Photosynthetic and chemosynthetic prokaryotes as primary producers. When the assimilation of "dead" energy (light energy or inorganic substrates) is coupled with the assimilation of inorganic carbon, we speak of Two Types of autonomous nutrition: photosynthesis and Chemosynthesis. This forms the foundation of global metabolism and is a fundamental prerequisite for life on Earth.

Photosynthetic organisms drive the assimilation of electromagnetic energy arriving from extraterrestrial space. Although the leading role in photosynthesis belongs to Higher Plants and Algae rather than bacteria, let us not forget that Chloroplasts originated from bacteria.

Photosynthesis forms the foundation of the global carbon assimilation process. In particular, higher plants produce 10¹² t of cellulose annually, making it the primary organic product of photosynthesis. The second place is held by photosynthetic plankton. Although its biomass contains no more than 2% of the total organic carbon, aquatic ecosystems turn over at a very high rate, providing up to 40% of global primary production.

Data on the COMPOSITION OF THE picoplankton in the World Ocean suggest that the cyanobacterium Prochlorococcus marinus is the most abundant primary producer. In community with algae and green plants, cyanobacteria form the trophic core of the aerobic biosphere.

Chemosynthetic prokaryotes, which assimilate energy from the oxidation of inorganic substrates (ammonia, hydrogen, sulfide, etc.), play a secondary role in primary production on the Earth's surface as well as in the water Column of seas and oceans. However, they serve as the trophic core of underwater biosphere oases. Inhabitants of the subterranean niche also possess the capacity for chemosynthesis.

Prokaryotes as bioproducers of methane. Microbial decomposition of organic remains in waterlogged soils and sludges, as well as in the digestive systems of herbivores and wood-eating insects (primarily termites), leads to the accumulation of biogenic methane. At least 1% of the carbon contained in plant photosynthetic products is converted into methane.

Methanogenic archaea produce 10⁹ t of methane annually. Approximately half of it is oxidized by aerobic methanotrophic bacteria. The remaining methane enters the atmosphere, where, together with CO₂ and other greenhouse gases, it drives the greenhouse effect.

Over recent centuries, the concentration of atmospheric methane (70% of which is of biological origin) has increased from 0.7 to 1.7 ppm.

This is primarily driven by the expansion of cultivated areas devoted to rice paddies, as well as the growth in livestock populations of ruminants.

Thus, autotrophic methanogenic archaea, which utilize H₂ and CO₂, together with photosynthetic and chemosynthetic bacteria, link the downward branch of the biological carbon cycle with the upward branch.

Prokaryotes as bioproducers of oxygen. In accordance with the overall equation of oxygenic photosynthesis (CO₂ + 2H₂O —> [CH₂O] + H₂O + O₂), biogenic oxygen is equimolecular to the assimilated carbon; that is, cyanobacteria together with plants generate 10¹¹ t of oxygen annually.

Over hundreds of millions of years, cyanobacteria have driven global biogeochemical changes. Specifically, they prepared the conditions for the emergence and biological progress of aerobes, ranging from microorganisms to higher plants and animals.

The earliest cyanobacteria were exposed to reactive oxygen species generated by their own activity—singlet oxygen, superoxide anion radicals, hydrogen peroxide, and hydroxyl radicals—whose accumulation leads to oxidative stress. Consequently, a prerequisite for the survival of these microorganisms was the acquisition of defense systems, among which aerobic respiration plays a crucial role.

Over a span of 2 billion years, cyanobacteria saturated the atmosphere with molecular oxygen, a byproduct of their metabolism. As a result, in the vivid phrasing of G. A. Zavarzin, the biosphere "turned inside out." Instead of oxygen pockets within an anaerobic environment, anaerobic pockets formed within an oxygen-rich environment. pH and redox gradients emerged in the upper layers of the Earth's crust, allowing prokaryotes to diversify their metabolism and, together with other microorganisms, weave a complex trophic network.

Prokaryotes as diazotrophs. The amount of nitrogen annually converted from its free molecular form into ammonium and nitrate forms is 2 • 10⁸ t. According to rough estimates, 15% of nitrogen is fixed in the atmosphere through the action of hard ultraviolet radiation and lightning discharges, while 25% is accounted for by industrial synthesis. The remaining 60% of fixed nitrogen results from the enzymatic reduction of molecular nitrogen to ammonia. This reaction is catalyzed by free-living and symbiotic diazotrophic bacteria.

The ability to fix nitrogen is characteristic of many phototrophic, chemolithotrophic, and chemoorganotrophic bacteria. In addition, diazotrophs have been discovered in the domain Archaea (for example, Methanobacterium thermolithoautotrophicum and Methanosarcina barkeri).

A special place among diazotrophs belongs to cyanobacteria, which utilize the products of oxygenic phototrophy in this process—ATP and an electron donor (reduced ferredoxin or NADPH). Although all known types of nitrogenases are inactivated by oxygen, cyanobacteria possess protective mechanisms that allow these enzymes to maintain activity even during endogenous oxygen production.

The primary contribution to global diazotrophy is made by filamentous cyanobacteria. In particular, Trichodesmium sp. strains provide other planktonic forms in (sub)tropical waters with fixed nitrogen. According to available data, this cyanobacterium alone accounts for 6% of global diazotrophy, which is at least 20% of the productivity of rhizobial ROOT-nodule bacteria.

Prokaryotes as regulators of biogeochemical cycles and active drivers of geochemical processes. Owing to their capacity for efficient energy and substrate transformation, functional diversity, immense population sizes, and high reproduction rates, prokaryotes are active participants in geochemical processes.

Autotrophic bacteria and, to a much lesser extent, autotrophic archaea drive the upward limb of the carbon cycle, working alongside plants and phototrophic protists. At the same time, degradative bacteria (particularly soil actinomycetes), together with fungi and heterotrophic protists, catalyze the final processes of the downward limb of the cycle.

As for the cycles of nitrogen, sulfur, and iron, they are almost entirely controlled by bacteria that catalyze the redox transformations of these elements. Deposits of elemental sulfur and iron oxides were formed through the METABOLIC ACTIVITY OF cyanobacteria and anoxygenic phototrophic bacteria. The origin of carbonate sedimentary rocks, in turn, is closely linked to cyanobacterial metabolism.