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

Preface

Class="center">Science is boundless; every day brings forth new challenges, and university education should strive to ignite the desire to contribute one's share to the treasury of science.

From the transcript of D.I. Mendeleev's lectures on inorganic chemistry delivered at St. Petersburg University in 1889 (Tomsk, 1910)

A Preface is written so that the author may clarify their objectives and offer justification for shortcomings.

Let us begin with why a new textbook on microbiology was needed and why the title "Microbiology" is accompanied by the subtitle "The Biology of Prokaryotes."

Among the fundamental manuals on microbiology published in Russian over the past 35 years are: "Chemical Microbiology"

by A. Rose (1971); "The Microbial World" by R. Stanier, E. Adelberg, and J. Ingraham (1979); "Bacterial METABOLISM" by G. Gottschalk (1982); "Bacterial Structure" by B. V. Gromov (1985); "General Microbiology" by H. Schlegel (1972; 1987); "Bacterial Ecology" by B. V. Gromov and G. V. Pavlenko (1989); "Phototrophic Microorganisms" by E. N. Kondratieva, I. V. Maksimova, and V. D. Samuilov (1989); "Microbiology" by M. V. Gusev and L. A. Mineeva (1978; 1985; 1992; 1993); "Autotrophic Prokaryotes" by E. N. Kondratieva (1996); and "Lectures on Environmental Microbiology" by G. A. Zavarzin (2003)*.

* In the second half of 2005, when the textbook was already in production, Mir Publishers released a Russian Introduction/27.html">Translation of the two-volume guide "Biology of the Prokaryotes" (J. W. Lengler, G. Drews, H. G. Schlegel, eds. Stuttgart: G. Thieme Verlag, 1999). We leave it to the readers to judge the merits and flaws of this book, co-authored by 43 specialists from Europe and the New World.

The more recent ones cover the subject only in specific aspects, while the earlier ones are outdated.

Furthermore, in all microbiological textbooks, very little attention is paid to functional Cytology, although understanding the specifics of prokaryotes without it is impossible.

Finally, there are the shortcomings of omissions, schematism, and brevity that generally characterize educational literature.

The present textbook examines all major aspects of microbiology (the biology of prokaryotes), systematically organizing information on the Organization and life processes of Bacteria and archaea in a way that will interest both the lay reader and the specialist. On A number of issues, the author holds a distinct personal viewpoint, since in higher education, established truths exist side by side with problems far from final resolution.

Among biologists, it is widely believed that prokaryotes differ from eukaryotes solely in their lack of a Nucleus. Sometimes it is added that prokaryotes lack compartmentalization and a Cytoskeleton. However, the distinction between PROKARYOTES AND EUKARYOTES runs much deeper.

Moreover, recent data are blurring the once-sharp boundary between prokaryotes and eukaryotes. First, it has been discovered that prokaryotes do possess compartmentalization and a cytoskeleton. Second, archaeal genomes have been found to contain homologs of eukaryotic genes. Third, prokaryotes have been shown to possess typical eukaryotic linear Chromosomes, as well as genomic infrastructure elements such as introns.

In light of the above, the objective of the textbook is to characterize the following aspects of prokaryotic biology:

— their place among biological entities;

— evolution and phylogeny;

— biodiversity and Classification;

— Structure and Functional properties;

— ecology;

— biogeochemical role and practical significance.

Although prokaryotes are used as model objects in many fields of modern biology, their structure and physiology are of primary interest mainly to microbiologists. Such informational discrimination is paradoxical at the beginning of the 21st century, when awareness of the role prokaryotes play in geochemical processes, the biosphere, and biotechnology is steadily capturing the public consciousness. Let us recall that we know about the pathogenic properties of bacteria not only from personal experience, but also in connection with the threat of their military-terrorist use.

Be that as it may, the information explosion driven by advances in bacteriology elevates it to the status of a general biological discipline. It was precisely through The Study of bacteria in the 1970s that the revolutionary Concept of the three phylogenetic domains (Bacteria, Archaea, Eukarya) was formulated, fundamentally reshaping the foundations of Cell Theory.

The author did not aim to create a surrogate textbook on "general" microbiology that jointly examines such heterogeneous entities as prokaryotes, nucleated microorganisms, and Viruses.

The minimum objective was to fill the gaps in textbooks on microbiology, general cytology, genetics, physiological biochemistry, and ecology, where prokaryotes are described superficially or ignored altogether.

The maximum objective is to establish the parity of prokaryote biology and eukaryote biology as two distinct branches of cell biology.

The term “cell biology” (French: la biologie cellulaire), proposed in 1884 by the French histologist C. V. Carnoy, denotes the science dealing with structures and processes at THE CELLULAR LEVEL. Because prokaryotes are unicellular organisms, the terms “Prokaryotic Cell biology” and “prokaryote biology” are largely synonymous. However, they are not entirely identical, as prokaryote biology encompasses not only intraverted but also extraverted aspects of life activity, among which the most important are:

— structural, genetic, trophic, and regulatory interactions between homologous or heterologous prokaryotic organisms;

— the existence of prokaryotes in symbiotic associations with nucleated organisms and viruses;

— the physicochemical impact of prokaryotes on their abiotic environment;

— the geochemical activity of global prokaryotic populations;

— The Use of prokaryotes in research on nucleated organisms;

— the use of prokaryotes in biotechnology.

For a long time, the zoological-botanical paradigm was applied to prokaryote biology, despite the fact that these organisms are structurally different from animal or PLANT Cells AND possess distinct functional properties. Today, we are witnessing revolutionary changes in prokaryotic systematics, as well as in conceptual views on their biodiversity and phylogeny. Traditional concepts regarding prokaryotic Abundance, the niches they occupy, their geographic distribution, and their biogeochemical role are being thoroughly revised. In terms of the depth to which cellular mechanisms and structures have been studied, “prokaryology” has not only caught up with “eukaryology” but in many respects has left it behind.

Nevertheless, in the ranking of biological objects, prokaryotes occupy a position inadequate to their real significance. This is primarily manifested in the “eukaryotic bias” of biological education. It is no longer a valid justification that until the early 1960s, bacteria were regarded as a group of lower plants, and summary information about them was confined to introductory chapters in botanical textbooks.

To most biologists, bacteria remain the outsiders of the living world. They have acquired a reputation as primitive creatures with exotic physiology that, under favorable conditions, are capable of rapid and potentially unlimited reproduction. A partly justified belief has emerged that studying bacteria requires the inductive method and practical skills to a greater extent than working with animals and plants—skills unnecessary for zoological and botanical research. This is explained not only by the microscopic size and physiological lability of bacteria, but also by the fact that their isolation and cultivation involve special Procedures, most notably the maintenance of sterility, which is not mandatory in zoological and botanical studies.

Following the path paved in the second half of the 19th century by the great microbiologists Louis Pasteur and Robert Koch, bacteriology initially addressed primarily anthropocentric problems. From its very inception, it acquired an applied character, focusing on pathogenic forms as well as agents used in food production or responsible for food spoilage.

It was not until the close of the 19th century that the great microbiologist S. N. Winogradsky drew attention to the problems of bacterial ecology. Concurrently, following the discoveries of Martinus Beijerinck, the last of the “big four,” interest awakened in the biodiversity of those bacteria lacking obvious utilitarian significance. The biochemistry of bacteria began to develop in the early 20th century, followed later, in the mid-1970s, by bacterial molecular biology. However, as before, the primary focus remains on

the STRUCTURE AND Functions of “high-profile” bacteria—medically important species and industrial producers. Acquiring information about bacteria that play no role in medicine and biotechnology is still not regarded as a fundamental task. Biochemists, molecular geneticists, and immunologists dealing with higher eukaryotes are convinced that the study of bacteria should be restricted to the specific problems of their own disciplines. Naturally, this perspective persists given the widespread use of Genomics Methods based on cloning animal and plant genes within bacterial replicons.

However, one should not forget that the ultimate goal of biology is the systemic analysis of living organisms and paleontological records; that is, bacteria and archaea are no less interesting than protists, Fungi, animals, plants, and viruses. On a planetary scale, prokaryotes constitute the trophic foundation of the biosphere, drive the cycles of carbon, nitrogen, oxygen, sulfur, phosphorus, iron, manganese, and other biogenic elements, and act as agents of global geochemical changes and morphological transformations in the upper layers of the Earth's crust. Despite their gigantic diversity, nucleated organisms, especially higher ones, play a subordinate role in these processes.

Notably, The Role of outsiders once played by bacteria has now fallen to archaea. The explanation remains the same: pathogenic forms are absent among them, they are not yet widely integrated into industrial production, and they are hardly used in molecular genetic experiments involving nucleated organisms.

Although archaea are phylogenetically unrelated to bacteria, they are discussed alongside them not only in textbooks—even specialized literature, most notably Bergey's Manual of Systematic Bacteriology (2001), follows this inconsistent tradition. The reason is that a convergent Structural and functional similarity exists between Representatives of the prokaryotic domains Archaea and Bacteria; most importantly, they share the same type of compartmentalization, whereas in eukaryotes it is achieved differently. In the prokaryotic cell, all three stages of genetic material Processing (Replication, Transcription, and translation) are localized within the cytoplasmic compartment and are not separated in time, whereas in nucleated cells, replication and transcription occur in the nucleoplasm, while translation takes place in the Cytoplasm. And although “archaeology” (archaeology of cells) is evolving into an independent discipline, educational literature still reflects a past stage of microbiological development when the archaeal concept did not yet exist and archaea were considered bacteria, albeit possessing a number of unique PHYSIOLOGICAL AND BIOCHEMICAL features.

The blame for the fact that prokaryotic cytology remains uninteresting not only to zoologists and botanists, but also to the majority of microbiologists, lies with educational curricula, even though a cursory comparison of prokaryotes with eukaryotes shows that they represent alternative types of Cellular Organization: prokaryotic cytology is a “different” cytology, and prokaryotic physiology differs fundamentally from that of The Eukaryotic Cell.

In Conclusion, it should be noted that biodiversity is fundamentally anchored by “mitochondrial” animals as well as plants, whose cells contain Plastids alongside Mitochondria. Since these Organelles exhibit a bacterial morphotype in structure and belong to the phylogenetic domain Bacteria in their evolutionary origin, an introduction to prokaryote biology provides a deeper understanding of their nature.

This textbook is based on the author's 30 years of experience delivering the general course “Microbiology,” as well as specialized courses including “Archaea,” “Lithotrophic Microorganisms,” “Prokaryotic Metabolism,” “Industrial Microbiology,” “Prokaryotic Systematics and Biodiversity,” “Cyanobacteria,” and “Prokaryotic Cytogenetics.”

The material of the textbook is divided into three volumes.

Volume I:

— history of prokaryote research;

— position in the metasystem;

— biological significance;

— systematics, biodiversity, and global niches;

— cytology.

Volume II:

— fundamentals of Nutrition;

— chemotrophy;

— phototrophy;

— autotrophy;

— key biosyntheses.

Volume III:

— cytogenetics;

— ontogeny;

— regulation;

— autoecology and synecology;

— natural population patterns;

— cultivation and growth in culture;

— fundamentals of biotechnology.

The author is deeply indebted to his mentors, domestic and foreign colleagues, as well as the staff of the Department of Microbiology at St. Petersburg State University. Most of all, he is grateful to those whose support, advice, assistance in text editing, and preparation of illustrations contributed the most to the creation of this textbook — his wife T. V. Sergovskaya and his daughter A. A. Pinevich.