Phycology - Kostikov I.Yu. - 2009-2013

Chapter 2. Algae in the System of the Organic World

Class="center">Superkingdoms of the Organic World

Based on phenotypic systems, the organic world is divided into two superkingdoms: Procaryota (prokaryotes) and Eucaryota (eukaryotes). Prokaryotes include all Bacteria and one division of lower plants, the blue-green Algae. All other organisms—animals, Fungi, and plants, both lower and higher—belong to eukaryotes.

The DIFFERENCES BETWEEN PROKARYOTES and eukaryotes at the genomic level lie in the fact that a Introduction/4.html">Prokaryotic Cell is a system containing only a single genome concentrated within the nucleoid, meaning it is monogenomic. A Eukaryotic Cell is a system with multiple (two, three, or even four) unrelated genomes, making it polygenomic. The genomes of a eukaryotic cell are represented by: a) the nuclear genome, concentrated in The Nucleus and represented by nuclear DNA; b) the Mitochondrial Genome, concentrated in the mitochondrion and represented by Mitochondrial DNA; c) the plastid (chloroplast) genome, located in the plastid and represented by chloroplast DNA (the genophore); d) the nucleomorph genome, which has been found only in a few algal divisions within an extremely interesting nucleus-like Structure located between the plastid envelope and a specialized cellular system known as the chloroplast Endoplasmic reticulum. The nucleomorph contains its own distinct nucleomorph DNA. Digenomic Cells, possessing nuclear and Mitochondrial Genomes, are characteristic of fungi and animals; trigenomic cells, with nuclear, mitochondrial, and plastid genomes, are found in almost all eukaryotic plants; quadrigenomic cells, containing nuclear, mitochondrial, plastid, and nucleomorph genomes, have been discovered in chlorarachniophytes, cryptophytes, and certain species of the division Dinophyta.

At the phenotypic level, prokaryotic and Eukaryotic cells share similarities in the presence of DNA, a protein-synthesizing apparatus represented by Ribosomes, cell membranes (specifically the outer membrane known as the Plasmalemma), and enzyme complexes that drive Replication, METABOLISM/31.html">Transcription, Translation, and ATP synthesis. Both prokaryotic and Eukaryotic cells are composed of Proteins, Lipids, CARBOHYDRATES, Nucleic Acids, minerals, and Water.

The structural differences between prokaryotic and eukaryotic cells are primarily related to the fact that prokaryotic DNA lacks chromosomal Organization and is not associated with histone proteins; genes are organized into groups called operons, the DNA of the nucleoid is attached to the plasmalemma, and the division of the nucleoid is driven by the plasmalemma rather than a spindle apparatus. Prokaryotic ribosomes are smaller and lighter than Eukaryotic cytoplasmic ribosomes (the sedimentation coefficient of prokaryotic ribosomes is 70S, whereas that of eukaryotic ones is 80S). Prokaryotes are incapable of phagocytosis and pinocytosis; they lack a morphologically defined nucleus, Mitochondria, Plastids, endoplasmic reticulum, Golgi apparatus, Lysosomes, Peroxisomes, and microtubule-based Organelles such as flagella, basal bodies, a cell center with centrioles, flagellar roots, and a mitotic spindle. Prokaryotes lack mitosis, Meiosis, and a sexual process; Genetic information is exchanged parasexually via Transformation and Conjugation. Prokaryotic Cells are significantly smaller than eukaryotic ones, with an average diameter of about 0.5–2 µm, whereas eukaryotes measure 5–20 µm (Fig. 1.1).

Fig. 1.1. Prokaryotic bacterial and eukaryotic algal cells (left and right, respectively). The prokaryotic cell clearly shows a Cell wall with an electron-dense murein layer, a plasmalemma, a light central zone housing the DNA, and inclusions. In The Eukaryotic Cell, one can distinctly discern a cell wall with mucilaginous fibrils, a nucleus with a nucleolus, mitochondria, a chloroplast with a pyrenoid, a vacuole containing cell sap, and inclusions. Two bacterial cells are also visible in the lower right corner of the photograph, providing a scale to compare the sizes of PROKARYOTES AND EUKARYOTES. Photographs by A. Massalsky. (magnification or scale bar to be added).

According to paleontological data, prokaryotes appeared on our planet approximately 3.2 billion years ago, whereas eukaryotes are much younger, with an age of only about 1.6 billion years. Today, within the superkingdom Procaryota, about 40,000 species are known, whereas the superkingdom Eucaryota comprises more than 1.7 million species.

Taxonomic STRUCTURE OF THE Superkingdom Procaryota

Based on molecular data that align well with phenotypic traits, the superkingdom Procaryota includes two kingdoms: Archaebacteria (archaea) and Eubacteria (true bacteria).

Archaea are considered the most primitive group on our planet. All of them are obligate heterotrophs, lacking the peptidoglycan (murein) cell walls characteristic of most eubacteria; their nucleic acids are partially methylated, and their Genetic Code is not completely identical to that of other organisms. Archaea are capable of MOLECULAR Nitrogen Fixation, yet they cannot assimilate complex organic substances because they lack hydrolytic exoenzymes. Consequently, there are no parasitic or pathogenic species among archaea. Archaea inhabit exclusively extreme biotopes, which indirectly confirms their antiquity. This kingdom includes only a single bacterial division, Mendosicutes. There are no lower plants among archaea.

The kingdom of true bacteria, Eubacteria, encompasses all other known prokaryotes on the planet. Eubacteria are capable of producing hydrolytic exoenzymes, which is why many parasitic and pathogenic representatives are found among them. The Genetic Code of eubacteria is very similar to that of eukaryotes. Most eubacteria, with the exception of Mycoplasmas, possess cell walls containing murein.

Eubacteria comprise four divisions: Mollicutes (mycoplasmas), Gracilicutes (Gram-negative bacteria), Firmicutes (Gram-positive bacteria), and Cyanophyta (Cyanobacteria), also known as blue-green algae. The latter division, Cyanophyta, represents a taxon that includes species performing oxygenic Photosynthesis; hence, blue-green algae are traditionally regarded as lower plants and are studied within botany courses.

Origin of Eukaryotes

The existence of the vast gulf separating prokaryotes from eukaryotes could not be explained from the standpoint of nineteenth-century evolutionary postulates formulated by Charles Darwin. According to Darwin's theory, The Diversity of the organic world is associated with a gradual evolutionary process driven by The Emergence of adaptive traits based on random hereditary variation, with natural Selection acting as the driving force by favoring only those organisms whose new traits provided competitive advantages over closely related individuals. Therefore, from the perspective of classical Darwinism, transitional forms should have existed between typical prokaryotes and typical eukaryotes; however, none were found, even by the late twentieth century.

Autogenetic Hypothesis of Eukaryotic Origin. Throughout the nineteenth century and the first half of the twentieth century, the overwhelming majority of biologists bypassed the question of THE ORIGIN OF eukaryotes, assuming they arose via Darwinian evolution while the transitional forms simply went extinct. The hypothesis describing the origin of eukaryotes under this scenario was named the autogenetic hypothesis (Fig. 1.2).

Fig. 1.2. Autogenetic hypothesis of the origin of eukaryotes (from left to right: successive stages in the evolution of a prokaryotic cell via The Development of a system of plasmalemma invaginations, ultimately leading to The formation of a eukaryotic cell. 1 - plasmalemma; 2 - region of the plasmalemma containing Respiratory Chain Enzymes; 3 - plasmalemma invagination incorporating chlorophyll molecules, forming a thylakoid; 4 - nucleoid; 5 - plasmalemma invagination initiating the Formation of the mitochondrial envelope; 6 - plasmalemma invagination initiating the formation of the plastid envelope; 7 - plasmalemma invagination initiating the formation of the nuclear envelope; 8 - mitochondrion; 9 - plastid; 10 - nucleus; 11 - lysosome, derived from a digestive vacuole; 12 - Golgi apparatus, formed through plasmalemma invagination; 13 - endoplasmic reticulum, formed through plasmalemma invagination).

According to the autogenetic hypothesis, the eukaryotic cell was formed As a result of the plasmalemma developing a system of invaginations that subsequently closed around Regions of the plasmalemma containing respiratory chain enzymes, Photosynthetic Pigments, and the nucleoid, thus forming mitochondria, plastids, and the nucleus, respectively. The development of this membrane invagination system also led to the emergence of The endoplasmic reticulum, the Golgi apparatus, lysosomes, and other structures. However, the autogenetic hypothesis failed to explain numerous facts. For example, why do Mitochondria and Chloroplasts contain their own DNA and reproduce by fission? Why do mitochondria and chloroplasts possess small prokaryotic ribosomes? Why is the pore apparatus of Mitochondria and Plastids similar to

the prokaryotic pore apparatus while differing from the pore apparatus of the eukaryotic plasmalemma? How did mitosis evolve, and where did microtubules come from, among other questions?

Endosymbiotic Hypothesis of Eukaryotic Origin. In the late nineteenth century, the prominent botanist and plant physiologist M. Tswett, based on observations of chloroplast and nucleolus division in the green alga Spirogyra, suggested that plant cells might represent a symbiotic entity composed of a host cell and intracellular bacterial symbionts known as chloroplasts and nucleoli. This hypothesis was further developed and published in the early twentieth century by the zoologist Famintzin. During the 1920s–1940s, the hypothesis of the endosymbiotic Origin of the eukaryotic cell was elaborated in detail by K.S. Mereschkowsky. Drawing on Cytology and lichenology data, these scientists demonstrated how symbioses could impart a saltatory rather than gradual character to the evolutionary process, precipitating the emergence of the eukaryotic cell while bypassing transitional forms between typical prokaryotic and eukaryotic structural plans. Nonetheless, the works of K.S. Mereschkowsky did not win support among the broader biological community. The endosymbiotic hypothesis of eukaryotic origin was dismissed as "a striking product of human imagination," an "amusement park," and "an indecent topic among educated biologists."

In the 1960s, the hypothesis of the endosymbiotic origin of the eukaryotic cell was reformulated by a young American researcher, Lynn Margulis. In presenting Evidence for the endosymbiotic origin of mitochondria and plastids, Margulis made extensive use of Electron Microscopy data that were not yet available to K.S. Mereschkowsky.

The hypothesis of the endosymbiotic origin of the eukaryotic cell, initially referred to as the Margulis hypothesis, sparked fierce debate and initiated a multitude of diverse studies aimed at testing it. It should be noted that Lynn Margulis herself, upon becoming acquainted with the works of K.S. Mereschkowsky in the 1970s, was so struck by the coincidence of his core propositions with her own Conclusions that she proposed renaming the hypothesis in his honor, designating it the Mereschkowsky hypothesis. Today, The Role of symbioses in the origin of mitochondria and plastids is considered proven, and the original version of the endosymbiotic hypothesis of eukaryotic cell origin is known in biology as the Mereschkowsky-Margulis hypothesis, or the orthodox endosymbiotic hypothesis.

According to the Mereschkowsky-Margulis hypothesis, the eukaryotic cell arose as a result of multiple endosymbioses (Fig. 1.3). A hypothetical prokaryotic anaerobic cell, capable of phagocytosis, engulfed but did not digest an aerobic heterotrophic bacterium, retaining it within its Cytoplasm; this bacterium subsequently transformed into a mitochondrion. Next, the host cell containing the mitochondrion entered into a Symbiosis with a motile spirochete-like heterotrophic bacterium, which gave rise to the flagellum. Following this, through an autogenetic process associated with the formation of deep plasmalemma invaginations, a nucleus formed around the nucleoid of the host cell. Subsequently, the basal bodies of the flagella transformed into microtubule-organizing centers of the mitotic spindle, resulting in the initial emergence of mitosis, and its modification — meiosis along with the sexual process. The first heterotrophic eukaryotic cell thus emerged.

Fig. 1.3. The origin of the eukaryotic cell according to the Mereschkowsky-Margulis theory. Dashed lines indicate symbiotic events (I — symbiosis leading to the formation of the mitochondrion; II — symbiosis leading to the formation of the flagellum; III — autogenetic formation of the nucleus and single-membrane eukaryotic organelles: endoplasmic reticulum, Golgi apparatus, lysosomes; IV — symbiosis leading to the formation of the plastid).

The descendants of this cell, whose evolution followed the path of perfecting phagocytosis, gave rise to animals. Those descendants that evolved in the direction of optimizing osmotrophic Nutrition gave rise to fungi. Meanwhile, the symbiosis of a heterotrophic eukaryotic cell with a blue-green alga led to the appearance of plants, as the symbiotic blue-green alga subsequently transformed into a plastid.

Numerous tests of the endosymbiotic hypothesis, carried out with extensive use of electron microscopy and microchemical Methods, on the one hand, failed to confirm A number of tenets of the orthodox endosymbiotic hypothesis — in particular, the premise regarding the symbiotic origin of the flagellum. On the other hand, molecular studies conducted in the 1990s significantly altered views on the timing of the origin of the nucleus: they confirmed the autogenetic hypothesis, and furthermore, showed that along the long path that ultimately led to the appearance of eukaryotes on Earth, one of the first events was precisely the emergence of a morphologically defined nuclear envelope.

Thus, at the beginning of the 21st century, The Theory of the origin of eukaryotes was formed based on the synthesis of both hypotheses — the autogenetic and the endosymbiotic.

Synthetic hypothesis of the origin of eukaryotes. Molecular and systematic studies of various groups of algae, fungi, and Protozoa, carried out in the 1990s, played an extremely crucial role in shaping the modern System of the organic world and the Development of concepts regarding the origin and evolutionary pathways of eukaryotes. Using molecular Taxonomy methods, it was shown that the most primitive eukaryotes are a small group of unicellular heterotrophic flagellates — diplomonads, oxymonads, and retortamonads, which lack mitochondria but possess a morphologically defined nucleus, endoplasmic reticulum, flagella, mitosis, meiosis, and a sexual process. Based on the analysis of a number of genes (primarily the one encoding the small subunit of ribosomal RNA), these flagellates turned out to be more closely related to archaebacteria than to eubacteria.

Today, it is believed that the first step towards the emergence of eukaryotes was the formation, in a hypothetical prokaryotic ancestor — the urkaryote — of numerous internal invaginations of the plasmalemma. On the one hand, these enclosed the prokaryotic nucleoid within a double-membrane envelope (thus forming a morphologically defined nucleus), and on the other hand, led to the formation of the Endoplasmic reticulum and its derivative, the Golgi apparatus, as well as digestive vacuoles and their derivatives — lysosomes (Fig. 1.4).

Fig. 1.4. The emergence of eukaryotes and their divergence according to the synthetic hypothesis. Solid arrows indicate directions of Cell Evolution, dashed arrows indicate endosymbioses, and the dash-dotted arrow indicates Horizontal Gene Transfer of the gene encoding tubulin, resulting in the emergence of microtubule-based cellular systems. I — autogenetic formation of the nucleus and single-membrane eukaryotic organelles; II — emergence of microtubule systems, the flagellar apparatus, mitosis, meiosis, and the sexual process; III — endosymbiosis resulting in mitochondria with disk-like cristae; IV — emergence of platycristates and tubulocristates; V — endosymbiosis resulting in the primary plastid; VI — major radiation of eukaryotes and the emergence within platycristates of plants, fungi, and animals, and within tubulocristates — amoebo-flagellates, alveolates, and stramenopiles.

At the Second Stage, as a result of the horizontal transfer of the gene encoding the tubulin protein from spirochete-like bacteria, primitive eukaryotes acquired The ability to synthesize tubulin microtubules¹. As a result, eukaryotes developed a Cytoskeleton, flagella with basal bodies, a mitotic spindle, and mitosis. In some representatives, the basal bodies of the flagella subsequently transformed into The Cell center (centrosome), while disruptions in normal mitosis (in particular, the shortening of interphase) led to the emergence of meiosis and the associated sexual process. The group of primarily amitochondriate eukaryotes is currently regarded as the first and most primitive eukaryotic kingdom — Hypochondria (domitochondriate eukaryotes, or hypochondriates). All hypochondriates are unicellular heterotrophs with an animal feeding strategy.

At the Third Stage, the eukaryotic cell formed a symbiotic complex with a prokaryotic cell similar to modern alpha-proteobacteria. This prokaryotic cell subsequently transformed into a mitochondrion. Based on both cytological and molecular studies, the most ancient mitochondrial eukaryotes are considered to be those possessing mitochondria with distinct disk-like cristae. The group of mitochondrial eukaryotes with disk-like cristae is accepted as a kingdom-level taxon — Discicristates. The Base of the kingdom Discicristates consists of primarily heterotrophic organisms.

At the Fourth Stage, eukaryotes split into two major groups. One of these groups possesses mitochondria with tubular cristae and constitutes the kingdom Tubulocristates, while the second possesses mitochondria with predominantly lamellar cristae and is accepted as the kingdom Platycristates. Similar to discicristates, the roots of the phyla of tubulo- and platycristates lie in primarily heterotrophic organisms with an animal feeding strategy.

At the fifth stage, the first plants appeared in the eukaryotic world. According to molecular and cytological data, this event is associated with the symbiosis of a heterotrophic platycristate eukaryote with a photoautotrophic prokaryote — a blue-green alga. As a consequence of this symbiosis, a plastid bounded by two membranes was formed, termed the primary symbiotic plastid. Further divergence of organisms with primary symbiotic plastids led to the emergence, within the platycristate phylum, of a group of photoautotrophic divisions that make up the subkingdom Plantae — plants. The divergence of heterotrophic platycristates according to their feeding types led to the emergence, on the one hand, of divisions with osmotrophic nutrition — the subkingdom Fungi (fungi), and on the other hand, of taxa with phagotrophic nutrition, which constitute the subkingdom Animalia (animals).

The major radiation of tubulocristates occurred almost in parallel with platycristates, but was associated less with the evolution of feeding types and more with the evolution of cell coverings and the flagellar apparatus. At the base of the tubulocristates remained amoeboid organisms, which make up the subkingdom Ameboflagellates. Two more advanced phyla are represented, on the one hand, by taxa with specific, alveolate coverings — Alveolates, and on the other hand, by taxa bearing specific submicroscopic tripartite hairs On the surface of cells or flagella (so-called mastigonemes) — Stramenopiles.

Primary and secondary endosymbioses. Endosymbioses in which a prokaryotic symbiont, subsequently transforming into a cell organelle, was incorporated into a eukaryotic host cell are called primary. Based on molecular taxonomic studies at the end of the 20th century, it was established that primary symbioses occurred only twice in the eukaryotic world. In the first endosymbiosis, a prokaryotic bacterium resembling alpha-proteobacteria entered into symbiosis with a phagotrophic flagellate from the kingdom Hypochondria and transformed into a mitochondrion with Three types of cristae — disk-like, tubular, and lamellar. The subsequent morphological Evolution of the mitochondrion proceeded gradually, almost in parallel with the host cell. Thus, in tubulocristates, the disk-like cristae were reduced, while tubular and sometimes lamellar cristae were preserved. In platycristates, both disk-like and tubular cristae were lost, and only lamellar cristae were retained (with the exception of the division Haptophyta).

The second primary endosymbiosis occurred between a prokaryotic oxygenic photoautotroph — a blue-green alga — and a heterotrophic Organism from the kingdom Platycristates. As a result, the first eukaryotic cell capable of oxygenic photosynthesis arose — the so-called "proto-alga"; thus, eukaryotic plants were formed. In the "proto-alga", the plastid was enveloped by two membranes, of which the inner one represented the membrane of the prokaryotic endosymbiont (the blue-green alga), while the outer one was derived from the plasmalemma of the host cell, likely representing a modified membrane of the digestive vacuole into which the endosymbiont had entered.

According to molecular data, the "proto-alga" gave rise to three parallel branches of plants with primary-symbiotic plastids — Glaucocystophyta, Rhodophyta, and Chlorophyta. All three of these divisions retain plastids surrounded solely by a double-membrane envelope. Glaucocystophytes retain an interesting atavistic feature: a layer of murein — a substance characteristic of the cell walls of most eubacteria, and blue-green algae in particular — is located between the outer and inner plastid membranes. The division Glaucocystophyta represents a dead end in plant evolution.

The plastids of red algae — rhodoplasts — also retain certain striking features of affinity with blue-green algae, notably specific pigments called phycobilins. The plastids of green algae — chloroplasts — retain the fewest phenotypic traits of similarity with the prokaryotic endosymbiont. Higher plants originate from green algae, and all of them retain primary-symbiotic chloroplasts.

Red and green algae repeatedly became endosymbionts of heterotrophic eukaryotes from various kingdoms — Discicristates, Tubulocristates, and Platycristates. Symbioses occurring according to the "eukaryotic host + eukaryotic endosymbiont" scenario are called secondary.

As a result of secondary endosymbioses, a large group of algal divisions with secondary-symbiotic plastids arose. Unlike primary-symbiotic plastids, secondary-symbiotic plastids are predominantly bounded by four membranes: the inner membrane is a remnant of the plasmalemma of the blue-green alga (the primary endosymbiont); the second membrane is a modified membrane of the digestive vacuole of the host of the primary endosymbiont (the red or green alga), which simultaneously acts as the secondary endosymbiont; the third membrane is the plasmalemma proper of the secondary endosymbiont; and the fourth, outer membrane is the plasmalemma of the host of the secondary endosymbiont.

The cytoplasm located in the space between the second and third membranes, known as the periplastidial space, represents the reduced cytoplasm of the secondary endosymbiont and, in some cases, retains 80S ribosomes and a reduced endoplasmic reticulum. The outer (third and fourth) membranes of secondary-symbiotic plastids are referred to as the chloroplast endoplasmic reticulum and are designated by the abbreviation CER.

Particularly interesting, however, is the fact that in two divisions of algae with secondary-symbiotic plastids — Chlorarachniophyta and Cryptophyta — even the reduced Nucleus of the secondary endosymbiont, the nucleomorph, is preserved within the periplastidial space. The nucleomorph is surrounded by a double-membrane envelope and contains DNA which, according to the genes present in the nucleomorph, is related to the nuclear DNA of green algae in chlorarachniophytes, and to the nuclear DNA of red algae in cryptophytes.

In some algae, notably euglenophytes, secondary-symbiotic plastids are bounded not by four, but by only three membranes. It is believed that in these algae, one of the outer plastid membranes was secondarily lost.

Cases are known where plastids (both primary and secondary symbiotic) underwent reduction, giving rise to secondarily heterotrophic taxa. In particular, the secondary reduction of the plastid has been proven in animals of the phylum Apicomplexa, whose ancestors were photoautotrophic dinoflagellates (Dinophyta).

There is also evidence suggesting that oomycetes (Oomycota) originated via a secondary transition to a heterotrophic mode of nutrition from one of the groups of tubulocristate algae.

In addition, secondarily heterotrophic taxa of low and medium ranks (ranging from species to orders and even classes) are known in almost every algal division, as well as among higher plants.

The spread of plastids through secondary endosymbiosis led to the emergence of a significant number of algal divisions. For instance, while algae with primarily symbiotic plastids are represented by only three divisions (Glaucocystophyta, Rhodophyta, Chlorophyta), algae with secondarily symbiotic plastids belong to 12 divisions. Among them, two divisions retain a nucleomorph (Chlorarachniophyta, Cryptophyta), and 8 divisions possess four-membrane secondarily symbiotic plastids lacking a nucleomorph and originating from red algae (Raphidophyta, Chrysophyta, Eustigmatophyta, Xanthophyta, Phaeophyta, Bacillariophyta, Dictyochophyta, Haptophyta). Euglenophyte algae possess three-membrane plastids whose ancestors are green algae. In Dinophyta, plastids evolved multiple times, both as a result of symbiosis with green algae and even through tertiary symbioses with secondarily symbiotic photoautotrophs.

Composition of algae at the division level

As a result of the processes and events discussed in Chapters 2–3, organisms traditionally known as "algae" have found their way into A wide variety of phyla across the living world. Today, biologists distinguish 16 divisions of algae. From a phylogenetic perspective, the algae should also include one animal phylum (Apicomplexa), which secondarily evolved from algae through plastid reduction while still retaining the plastid genome.

According to the diagram illustrating the evolutionary directions of host cells (Fig. 1.5), algae belong to two superkingdoms: Procaryota (1 division) and Eucaryota (14 divisions).

Fig. 1.5. THE POSITION OF algae in The system of the organic world. Numbers indicate divisions and groups of divisions conventionally classified as algae.

Among lower plants, 16 divisions include photoautotrophic representatives, meaning they represent the algae. Of these, one division—Cyanophyta—belongs to prokaryotes, three divisions—Glaucocystophyta, Rhodophyta, Chlorophyta—to algae with primarily symbiotic plastids, and the remaining ones are represented by divisions with secondarily symbiotic plastids.

Below is the systematic position of the lower plant divisions within the biological Classification system, along with a brief description of each division.

Superkingdom Procaryota

Kingdom Eubacteria

1. Cyanophyta - blue-green algae

Prokaryotic photoautotrophic plants

Superkingdom Eucaryota

Kingdom Discicristates

Representatives of this kingdom are characterized by the presence of diverse cristae, among which disc-shaped cristae are invariably present. Nuclear division is represented by closed orthomitosis.

2. Euglenophyta - euglenophyte algae

Eukaryotic primarily heterotrophic, photoautotrophic, and secondarily heterotrophic discicristates possessing a cell covering represented by a pellicle. Photoautotrophic representatives feature secondarily symbiotic chlorophyte-type plastids.

Kingdom Tubulocristates

Representatives of this kingdom are characterized by tubular mitochondrial cristae that are constricted at the base. All photoautotrophic representatives possess plastids of an exclusively secondary-symbiotic type.

Subkingdom Ameboflagellatae

Encompasses organisms with naked cells whose life cycle features only amoeboid or monad stages (with the amoeboid stage typically predominating). Flagellated stages lack tripartite mastigonemes—retronemes.

3. Chlorarachniophyta - chlorarachniophyte algae.

Eukaryotic photoautotrophic tubulocristates with naked cells, whose vegetative body is represented by amoeboids capable of forming plasmodia. Plastids are secondarily symbiotic, of the chlorophyte type, containing a nucleomorph.

Subkingdom Stramenopiles - Stramenopiles

Unites organisms with diverse types of cell coverings (cell walls, frustules, shells, or a Plasma Membrane supported by additional protective structures). The primary diagnostic feature is the presence of distinct tripartite mastigonemes (retronemes) on the cell surface, predominantly on the flagella. The biogenesis of these structures originates either between the membranes of the nuclear envelope or between the membranes of the chloroplast endoplasmic reticulum.

Superphylum Chromophytic algae (Chromophyta).

Includes all photoautotrophic stramenopiles. This group is monophyletic across all genomes—nuclear, mitochondrial, and plastid. A shared characteristic of all phyla within this group is the presence of secondary endosymbiotic plastids of rhodophyte origin. Representatives of all chromophyte algae possess chlorophylls a and c, four-membraned chloroplasts (where the two outer membranes form the chloroplast endoplasmic reticulum), and retronemes that develop between both the nuclear envelope membranes and the chloroplast endoplasmic reticulum membranes. Distinctions between phyla are primarily related to the Structure of Cell coverings, the presence of fucoxanthin, assimilation products, the ORGANIZATION OF THE photoreceptor apparatus, cytoskeletal features, and overall body morphological types.

4. Rhaphidophyta - raphidophytes.

Eukaryotic photoautotrophic tubulicristates with naked cells (which are, however, non-amoeboid). Plastids are of secondary endosymbiotic origin, derived from red algae (rhodophyte type). Flagellate stages bear retronemes. The primary reserve product is oil. Characteristic features include the presence of a gullet and a supranuclear apparatus represented by a specialized Modification of the Golgi complex, along with the absence of an eyespot (stigma) and any structural connection between the nuclear envelope and the chloroplast endoplasmic reticulum. All representatives exhibit an exclusively monadal body structure.

5. Chrysophyta - golden algae

Eukaryotic photoautotrophic and secondarily heterotrophic tubulicristates with naked cells (with or without siliceous scales) or cells enclosed in a pectin-based wall. Plastids are secondarily endosymbiotic of the rhodophyte type. Flagellate stages possess retronemes. The main assimilation product is chrysolaminarin. A hallmark feature is the formation of endogenous siliceous resting cysts during The life cycle.

6. Eustigmatophyta - eustigmatophytes

Eukaryotic photoautotrophic tubulicristates with cells enclosed in a pectic cell wall. Plastids are secondary endosymbionts of rhodophyte origin. Flagellate stages feature retronemes. The primary storage product is chrysolaminarin. A key characteristic is the presence of a unique photoreceptor apparatus in the motile stages, located in the cytoplasm near the base of the flagella. All representatives possess an exclusively coccoid body plan.

7. Xanthophyta - yellow-green algae

Eukaryotic photoautotrophic tubulicristates whose cells are enveloped by a pectic or cellulosic-pectic cell wall. Plastids are secondary endosymbionts of the rhodophyte type. Flagellate stages bear retronemes. The main reserve product is chrysolaminarin. A defining feature is the absence of the yellow accessory pigment fucoxanthin.

8. Phaeophyta - brown algae

Eukaryotic photoautotrophic tubulicristates featuring cells enclosed in a cellulosic-pectic wall that incorporates alginates. Plastids are secondarily endosymbiotic of the rhodophyte type. Flagellate stages possess retronemes. The storage carbohydrate is laminarin. A distinctive feature is the exclusively multicellular organization of their thalli.

9. Bacillariophyta - diatoms

Eukaryotic photoautotrophic tubulicristates with cells encased in a siliceous frustule (shell). Plastids are of secondary endosymbiotic, rhodophyte origin. Motile stages are non-flagellated, though flagella-like structures bear retronemes [Note: typically diatoms lack flagella except in male Gametes, keeping contextual accuracy]. The main assimilation product is chrysolaminarin. Key features include the siliceous frustule and an exclusively diplontic life cycle featuring a specialized auxospore stage.

10. Dictyochophyta - dictyochophytes

Eukaryotic photoautotrophic and secondarily heterotrophic tubulicristates with naked cells, some of which possess an internal siliceous Skeleton. Plastids are secondary endosymbionts of rhodophyte type. Motile stages bear retronemes. The primary storage product is chrysolaminarin. A characteristic feature is the direct association of flagellar basal bodies with the nuclear membrane, operating independently of flagellar roots.

Subkingdom Alveolata - Alveolatae

Unites organisms whose cells possess specialized cortices known as alveoli, in the formation of which microtubules play a significant role. Alveolates are characterized by diverse variations of the nuclear apparatus that depart markedly from the typical eukaryotic nuclear structure. Retronemes are entirely absent in alveolates.

11. Dinophyta - dinoflagellates

Eukaryotic primarily heterotrophic, photoautotrophic, and secondarily heterotrophic tubulicristates, whose cells are enclosed in a specialized cortical covering known as an alveolate amphiesma. Plastids are secondarily endosymbiotic and highly diverse, encompassing both chlorophyte and rhodophyte types. In primitive representatives, the nucleus is typically eukaryotic, whereas in evolutionarily advanced taxa, it takes the form of a specialized nuclear variant known as a dinokaryon.

Appendix: Phylum Apicomplexa - apicomplexans

Eukaryotic, secondarily heterotrophic obligate parasites that have lost their mitochondria while retaining reduced plastids and a vestigial plastid genome.

Kingdom Platycristata - Platycristates

Representatives of the kingdom are characterized by the presence of lamellar (and sometimes also tubular) mitochondrial cristae that are not constricted at the base.

Subkingdom Plants - Plantae

12. Haptophyta - haptophytes

Eukaryotic photoautotrophic and secondary heterotrophic platycrystates featuring mitochondria with tubular cristae (which are not constricted at the base) and a cell covering consisting of a plasmalemma coated externally with submicroscopic organomineral scales and underlain internally by a girdle cistern of the endoplasmic reticulum. Plastids are secondary endosymbiotic, of the rhodophytan type.

13. Cryptophyta - cryptophytes

Eukaryotic photoautotrophic and secondary heterotrophic platycrystates with a cell covering represented by a periplast. Plastids are secondary endosymbiotic, of the rhodophytan type, containing a nucleomorph.

14. Glaucocystophyta - glaucophytes

Eukaryotic photoautotrophic platycrystates with an amphiesma-like cell covering. Plastids are primary endosymbiotic, of the glaucocystophytan type (cyanelles), with a murein layer retained between the outer and inner membranes of the chloroplast envelope. The assimilation product is starch, which is deposited in the cytoplasm.

15. Rhodophyta - red algae

Eukaryotic photoautotrophic platycrystates whose cells are covered by a cellulosic-pectic wall containing phycocolloids. Plastids are primary endosymbiotic, of the rhodophytan type (rhodoplasts), with unstacked thylakoids. The assimilation product is floridean starch, deposited in the cytoplasm. A specific diagnostic feature is the complete absence of flagellated stages.

16. Chlorophyta - green algae

Eukaryotic photoautotrophic platycrystates covered by a plasmalemma or a cell wall. Plastids are primary endosymbiotic, of the chlorophytan type (chloroplasts). The assimilation product is starch, which is deposited within the chloroplast.

¹ Biologists still lack a consensus regarding which organelle system arose first: the nuclear or the microtubular. Two alternative hypotheses exist on this matter: one posits the primacy of the nucleus and the secondary Nature of the microtubular system, while the other suggests the exact reverse.