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

INTRODUCTION. PROKARYOTES AS THE MAIN OBJECTS OF MICROBIOLOGY

Class="center">Quis potis est dignum pollenti pectore carmen

Condere pro rerum maiestate hisque repertis?

Quisve valet verbis tantum, qui fingere laudes

Pro meritis eius possit, qui talia nobis

Pectore parta suo quaesitaque praemia liquit?

(Who is able with a powerful soul to compose a song worthy

Of the majesty of things and these great discoveries?

Or who is so rich in words that he could fashion praise

Fitting the merits of him who left us such treasures,

Born of his own mind and won for our inheritance?)

Lucretius. De rerum natura

Today, the terms "prokaryotes" and "eukaryotes" are familiar not only to every biologist, but to anyone with a moderate education. Although more concrete than such terms as "life," "Cell," "Organism," and "evolution," they are not understood in the same way by everyone, and many misunderstand them altogether. Therefore, we must take a closer look at what they actually mean.

The fact is that the terms "prokaryotes" and "eukaryotes" refer to specific living organisms, each occupying a defined position in the taxonomic hierarchy. PROKARYOTES AND EUKARYOTES represent taxonomic groups of the highest rank used in megataxonomy.

Megataxonomy (from the Greek megas meaning great) is one of the most important branches of biology. It serves as a global framework for reconstructing the higher-level Phylogenetic relationships among living organisms.

Of all the megataxonomic schemes ever proposed, only one has stood the test of time: the dichotomous system introduced by the French protistologist Édouard Chatton. In a collection of works published in 1937, he regarded The Nucleus as the primary distinguishing feature for classifying cellular morphotypes. Organisms with a distinct nucleus in their Cells he named "eukaryotes" (from the Greek eu meaning good and karyon meaning kernel or nucleus), whereas organisms whose cells lack differentiation into a nucleus and Cytoplasm were designated "prokaryotes" (from the Greek pro meaning before and karyon meaning kernel or nucleus). Today, the terms "eukaryotes" and "prokaryotes" have acquired an expanded

meaning, reflecting not merely the formal presence or absence of a nucleus, but distinct cytoarchitectonics—that is, the overall structural plan of The Cell that determines the Organization of its genetic, transport, metabolic, and regulatory systems.

Until the late 1970s, no one suspected that organisms located far apart on the evolutionary tree could share convergent cytological traits, including such a negative trait as the absence of a nucleus. Currently, two distinct groups of prokaryotes of different evolutionary origins are recognized: Bacteria and archaea.

To fully grasp the meaning of the term "prokaryotes," we must explore the topics of global cellular morphotypes and global phylogeny.

First of all, it is necessary to outline the subject matter and Methods of microbiology. Classical microbiology and modern science under the same name differ not only in their theoretical depth and the volume of accumulated facts, but also in how they define their core subject.

Classical microbiology contrasted microorganisms with macroorganisms while ignoring the organizational and phylogenetic status of both. Therefore, we must first clarify the exact meaning of the terms "microbe," "prokaryote," "bacterium," and "archaeon."

Due to the frequent misuse of the term "prokaryote," let us analyze it critically. This is all the more necessary because the original interpretation of the term (= a cell without a nucleus), as well as the structural and phylogenetic content attributed to it in the mid-1960s (= bacterium), no longer correspond to the Current state of evolutionary Cytology and represent an obsolete stage in The history of science.

It is worth recalling that the term "biology" was introduced between 1802 and 1816 by the German botanist Gottfried Reinhold Treviranus in his six-volume work Biologie oder Philosophie der lebenden Natur. It was subsequently adopted by Jean-Baptiste de Lamarck.

The METABOLISM/13.html">History of the term "microbiology" is quite interesting. Contrary to the phonetic tradition of placing the stress on the first syllable, it is not interpreted as "minor biology," but rather as the "science of microbiotas" or "the science of small forms of life" (from the Greek microbios meaning small living creature, and logos meaning study). When using this term, we often overlook the fact that the size category "micro-" is relative (there are both relatively and absolutely small living beings; for instance, humans are not considered objects of microbiology, even though they are orders of magnitude smaller than the largest animals and plants, such as the blue whale and the giant sequoia).

The term "microbe" (French microbe) was introduced by the French physician Charles-Emmanuel Sedillot (J. Sédillot). In a speech delivered on March 11, 1878, at a meeting of the Académie des Sciences entitled "The Influence of Mr. Pasteur's Discoveries on the Progress of Surgery," he deliberately referred to absolute microscopic entities. As for Pasteur himself, he called this science "microbie" (French microbie). It was only after the patron's death in 1895 that his coworker Émile Duclaux (E. Duclaux) proposed the term "microbiology" (French microbiologie), which soon became universally accepted.

Various Classification algorithms are known, serving as the basis by which biological disciplines divide their "spheres of influence." When the method takes precedence, we speak of systematics, Microscopy, biometry, molecular biology, and so on. If the primary role belongs to the level of organization or a specific aspect of Structure, we refer to cell biology, cytology, physiological biochemistry, genetics, and the like. Both of these approaches are eclectic. They emerged In the second half of the 19th century and the first half of the 20th century and, up to a certain point, ensured the integration of research on a relatively narrow range of objects using imperfect methodological tools.

The Subject Matter of biology is the world of living organisms in its unity and particulars; therefore, the criterion for the specialization of biological disciplines is the organization of objects that form objectively distinct systematic groups. The boundaries between them can be drawn by reconstructing phylogeny while adhering to the laws of logic and the formal rules of Taxonomy. In other words, the task of a specific biological discipline is to study a particular natural taxon.

Classical microbiology did not employ this algorithm. It studied all microscopic living objects (from Greek micros, meaning small, and scopia, meaning observation), i.e., those indistinguishable to the naked eye.

Based on this size criterion, the realm of microbes encompasses five groups of objects with different structures and, what is even more significant, with independent evolutionary origins:

— prokaryotes (phylogenetic domain Bacteria);

— "other" prokaryotes (phylogenetic domain Archaea);

— unicellular nuclear organisms (a collective group of protists comprising several dozen kingdoms);

— multicellular nuclear microorganisms (representatives of Fungi, Plantae, and Animalia — specifically, A number of fungi, filamentous Algae, and Flatworms);

— microscopic entities lacking a cellular structure (a collective group of Viruses and virus-like agents).

The phylogenetically heterogeneous group of protists is studied by protistology. The microscopic Representatives of the kingdoms of fungi, plants, and animals, which form the crown of the Phylogenetic Tree of nuclear organisms, constitute the subject matter of mycology, botany, and zoology, respectively. Similarly, non-cellular living entities are the subject of virology.

The primary object of study in microbiology is prokaryotes. However, this violates THE PRINCIPLE OF the phylogenetic unity of the subject that we proclaimed, since the prokaryote group consists of unrelated microorganisms — bacteria and archaea.

The discipline that studies bacteria is called bacteriology (from Greek bacteria, meaning staff, and logos, meaning study). The authorship of this term belongs to the German botanist Ferdinand Cohn (F. Cohn), who in 1875 referred to unicellular microorganisms that reproduce by binary fission and lack a nucleus as bacteria. The occurrence frequency of rod-shaped bacteria is no higher than that of spherical bacteria, or cocci (from Greek coccos, meaning grain). Merely by chance, or perhaps thanks to Cohn's philological intuition, there is no science with the curious name "coccology."

Regarding non-bacterial prokaryotes, the term "archaebacteria" (from Greek archaios, meaning ancient, and bacteria, meaning staff; "ancient bacteria") was used between 1977 and 1990. It was proposed by the American microbiologist Carl Woese (C. Woese). This unfortunate term created confusion, and Woese eventually replaced it with the term "archaea" (from Greek archaios, meaning ancient). Thus, the first misunderstanding associated with the term "archaebacteria" was corrected, since they do not belong to the phylogenetic domain Bacteria. However, a second issue remains, as the phylogenetic domain Archaea has no grounds to claim The Role of the most archaic (it formed after the domain Bacteria and is equivalent in age to the domain Eukarya).

On the global tree of life, archaeal prokaryotes are separated from bacterial prokaryotes, which gives "archaeotology" (from Greek archaios, meaning ancient, and logos, meaning study; "the science of archaea") the right to stand out as an independent discipline.

In the proposed textbook on the biology of prokaryotes, which jointly presents bacteriology and "archaeotology," the principle of the phylogenetic unity of the subject is not observed. What is the reason for this admitted eclecticism — an inadvertent miscalculation, a tribute to tradition, or are we dealing with inseparable Siamese twins?

The fact is that there has not yet been a modern textbook on the biology of prokaryotes in Russian. In addition, archaeotology has not yet completely separated from bacteriology. And finally, most importantly, bacteria and archaea share a number of phenotypic properties of both Divergent and convergent nature:

— they have similar cytoarchitectonics; specifically, they are compartmentalized in the same way, yet differently from eukaryotes;

— they share a great deal in the organization of functional subcellular structures;

— they possess similar metabolic and transport systems, as well as uniform regulatory processes;

— they reproduce by amitotic division and exist in nature as clonal populations; the microevolution of such genetic systems and the speciation processes based on them follow similar patterns.

Furthermore, bacteria and archaea are investigated using the same methods; identical screening strategies are used to analyze their biodiversity; and they are jointly considered in Bergey's Manual of Systematic Bacteriology. In any case, The Study of bacteria is closely and permanently intertwined with the study of archaea.

As prokaryotic biology explores new objects, THE CONCEPT OF the two groups of prokaryotes, bacteria and archaea, becomes increasingly convincing. However, further progress in this field remains unpredictable. Since not everyone agrees with the concept of archaea, it may still be revised — in whole or in certain details.