Eukaryotic Microbial Diversity

Phylogeny of the Eukarya

Eukaryotes are very diverse in phylogenic terms, the common feature being a membrane bound nucleus.

Learning Objectives

Assess the phylogeny of Eukarya

Key Takeaways

Key Points

  • Eukaryotes are broadly determined by the prescence of a membrane bound nucleus, though many eukaryotes have other membrane bound structures.
  • The domain of eukarya are broadly grouped into six kingdoms: Excavata, Amoebozoa, Opisthokonta, Rhizaria, Chromalveolata, and Archaeplastida.
  • The exact nature of the relationships (i.e. common ancestors) of the the eukarya domain are still debated.

Key Terms

  • crown group: In phylogenetics, the crown group of a collection of species consists of the living representatives of the collection together with their ancestors back to their last common ancestor as well as all of that ancestor’s descendants. It is thus a clade, a group consisting of a species and all its descendents.
  • cristae: Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes.

Phylogeny of the Eukarya

A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria, chloroplasts, and the Golgi apparatus. All large complex organisms are eukaryotes, including animals, plants, and fungi. The group also includes many unicellular organisms.

rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved crown group, which was usually divided by the form of the mitochondrial cristae. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive. But this is now considered an artifact of a divergent evolutionary line, and they are known to have lost them secondarily.

Eukaryotes are split into 6, subdivisions, referred to as kingdoms. They include:

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The Six Kingdoms: This is one hypothesis of eukaryotic relationships. The Opisthokonta group includes both animals (Metazoa) and fungi. Plants (Plantae) are placed in Archaeplastida.

1. Excavata – Various flagellate protozoa

2. Amoebozoa – Most lobose amoeboids and slime moulds

3. Opisthokonta – Animals, fungi, choanoflagellates

4. RhizariaForaminifera – Radiolaria, and various other amoeboid protozoa

5. ChromalveolataStramenopiles (or Heterokonta) – Haptophyta, Cryptophyta (or cryptomonads), and Alveolata

6. Archaeplastida (or Primoplantae) – Land plants, green algae, red algae, and glaucophytes

There is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizara is not one of the main eukaryote groups. The Amoeboza and Opisthokonta are each monophyletic and form a clade, often called the unikonts. There is debate about the true constituents of the animal kingdoms.

Beyond this, there does not appear to be a consensus. It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists. The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000 to 220,050 Mb in the dinoflagellate Prorocentrum micans. This suggests that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis), a dormant cyst with a cell wall of chitin, cellulose, and peroxisomes. Later endosymbiosis led to the spread of plastids in some lineages.

Historical Overview of Eukaryotes

Until more recent work, the historical view of eukaryotes has been anthropomorphic.

Learning Objectives

Examine the historical view of eukaryotes

Key Takeaways

Key Points

  • Plants and animals since ancient times have been considered to be related.
  • Initially, microscopic organisms were classified into plants or animals.
  • Genomic sequencing has reorganized our understanding of life, and how different eukaryotic clades are related.

Key Terms

  • kingdom: A rank in the classification of organisms, below domain and above phylum; a taxon at that rank (e.g. the plant kingdom, the animal kingdom).
  • clade: A group of animals or other organisms derived from a common ancestor species.

Even back to Antiquity the two clades of animals and plants were recognized. They were given the taxonomic rank of Kingdom (biology) by Linnaeus. Although he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980’s. The various single-cell eukaryotes were originally placed with plants or animals when they became known. The German biologist Georg A. Goldfuss coined the word protozoa in 1830 to refer to organisms such as ciliates and corals. This group was expanded until it encompassed all single-cell eukaryotes. They were given their own kingdom, the Protista, by Ernst Haeckel in 1866.

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Biological classification: The hierarchy of biological classification’s eight major taxonomic ranks. A genus contains one or more species. Intermediate minor rankings are not shown.

The eukaryotes came to be composed of four kingdoms: Kingdom Protista, Kingdom Plantae, Kingdom Fungi, and Kingdom Animalia. The protists were understood to be “primitive forms,” and thus an evolutionary grade, united by their primitive unicellular nature. The disentanglement of the deep splits in the tree of life only really got going with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain. As such the tree of life consists of three domains: Archaea, Bacteria, and Eukarya. The arrangement of taxa reflects the fundamental differences in the genomes, a less anthropomorphic “animal-centric” world view. At the same time, work on the protist tree intensified, and is still actively going on today. Several alternative classifications have been forwarded, though there is no consensus in the field.

Opisthokonts: Animals and Fungi

Opisthokonts include the animal and fungus kingdoms.

Learning Objectives

Describe Opistkokonts

Key Takeaways

Key Points

  • The unifying feature of opisthokonts is the presence of a flagellum, sometimes only ancestrally or at a specific point in the life cycle.
  • Genetic sequencing has confirmed that opisthokonts are genetically related.
  • Opisthokonts are split into two groups: holomycota (includes fungi), and holozoa (includes animals).

Key Terms

  • monophyletic: Of, pertaining to, or affecting a single phylum (or other taxon) of organisms.
  • flagellum: In protists, a long, whiplike membrane-enclosed organelle used for locomotion or feeding.

The opisthokonts, or “fungi/metazoa group”, are a broad group of eukaryotes, including both the animal and fungus kingdoms, together with the eukaryotic microorganisms that are sometimes grouped in the paraphyletic phylum choanozoa (previously assigned to the protist “kingdom”). Both genetic and ultrastructural studies strongly support that opisthokonts form a monophyletic group.

One common characteristic of opisthokonts is that flagellate cells, such as most animal sperm and chytrid spores, propel themselves with a single posterior flagellum. This gives the group its name. In contrast, flagellate cells in other eukaryote groups propel themselves with one or more anterior flagellae. Most fungi do not produce cells with flagellae, but the primitive fungal chytrids do, suggesting that a common ancestor of current fungal species did have a flagellum.

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Flagellum: Here is a depiction of a unicellular organism with a flagellum. Flagellum are a typical structure found on opisthokonts, sometimes at only specific points of the a life cycle.

The close relationship between animals and fungi was suggested by Cavalier-Smith in 1987, who used the informal name opisthokonta (the formal name has been used for the chytrids). The discovery was confirmed by later genetic studies. Early phylogenies placed opisthokonts near the plants and other groups that have mitochondria with flat cristae, but this character varies. Cavalier-Smith and Stechmann argue that the uniciliate eukaryotes such as opisthokonts and Amoebozoa, collectively called unikonts, split off from the other biciliate eukaryotes, called bikonts, shortly after they evolved.

Opisthokonts are divided into Holomycota or Nucletmycea (fungi and all organisms more closely related to fungi than to animals) and Holozoa (animals and all organisms more closely related to animals than to fungi); no opisthokonts basal to the Holomycota/Holozoa split have yet been identified.

Endosymbiotic Theory and the Evolution of Eukaryotes

Genome fusion occurs during endosymbiosis, which is the mechanism proposed as responsible for the first eukaryotic cells.

Learning Objectives

Describe the genome fusion hypothesis and its relationship to the evolution of eukaryotes

Key Takeaways

Key Points

  • Two symbiotic organisms become endosymbiotic when one species is taken inside the cytoplasm of another species, resulting in genome fusion.
  • Genome fusion, by endosymbiosis, between two species, one an Archaea and the other a Bacteria, has been proposed as responsible for the evolution of the first eukaryotic cells.
  • Gram-negative bacteria are proposed to result from an endosymbiotic fusion of archaeal and bacterial species through a mechanism that has also been used to explain the double membranes found in mitochondria and chloroplasts.
  • The nucleus-first hypothesis proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria.
  • The mitochondria-first hypothesis proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus to become the first eukaryotic cell.
  • The eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity.

Key Terms

  • genome fusion: a result of endosymbiosis when a genome consists of genes from both the endosymbiont and the host.
  • symbiotic: of a relationship with mutual benefit between two individuals or organisms
  • endosymbiosis: when one symbiotic species is taken inside the cytoplasm of another symbiotic species and both become endosymbiotic

Genome Fusion and the Evolution of Eukaryotes

Scientists believe the ultimate event in HGT (horizontal gene transfer) occurs through genome fusion between different species when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or, in other instances, when the mitochondria located in the flagellum of the sperm fails to enter the egg.

Within the past decade, the process of genome fusion by endosymbiosis has been proposed to be responsible for the evolution of the first eukaryotic cells. Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), it has been proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species: one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

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Endosymbiosis in eukaryotes: The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. More controversial is the proposal that (a) the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes; and that (b) Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane.

More recent work proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, did result from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. A lot of skepticism still surrounds this hypothesis; the ideas are still debated within the biological science community.

There are several other competing hypotheses as to the origin of eukaryotes and the nucleus. One idea about how the eukaryotic nucleus evolved is that prokaryotic cells produced an additional membrane which surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely-related to eukaryotes. Another hypothesis, the nucleus-first hypothesis, proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis, however, proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus (by fusion or other mechanisms) to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity. All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

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Three hypotheses of eukaryotic and prokaryotic evolution: Three alternate hypotheses of eukaryotic and prokaryotic evolution are (a) the nucleus-first hypothesis, (b) the mitochondrion-first hypothesis, and (c) the eukaryote-first hypothesis.

Cell Structure, Metabolism, and Motility

Protists are an incredibly diverse set of eukaryotes of various sizes, cell structures, metabolisms, and methods of motility.

Learning Objectives

Describe the metabolism and structure of protists, explaining the structures that provide their motility

Key Takeaways

Key Points

  • Protist cells may contain a single nucleus or many nuclei; they range in size from microscopic to thousands of meters in area.
  • Protists may have animal-like cell membranes, plant-like cell walls, or may be covered by a pellicle.
  • Some protists are heterotrophs and ingest food by phagocytosis, while other types of protists are photoautotrophs and store energy via photosynthesis.
  • Most protists are motile and generate movement with cilia, flagella, or pseudopodia.

Key Terms

  • amorphous: lacking a definite form or clear shape
  • multinucleate: having more than one nucleus
  • pellicle: cuticle, the hard protective outer layer of certain life forms
  • taxis: the movement of an organism in response to a stimulus; similar to kinesis, but more direct
  • phagocytosis: the process where a cell incorporates a particle by extending pseudopodia and drawing the particle into a vacuole of its cytoplasm
  • phagosome: a membrane-bound vacuole within a cell containing foreign material captured by phagocytosis

Cell Structure

The cells of protists are among the most elaborate and diverse of all cells. Most protists are microscopic and unicellular, but some true multicellular forms exist. A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways as a multicellular organism. Still other protists are composed of enormous, multinucleate, single cells that look like amorphous blobs of slime, or in other cases, similar to ferns. Many protist cells are multinucleated; in some species, the nuclei are different sizes and have distinct roles in protist cell function.

Single protist cells range in size from less than a micrometer to thousands of square meters (giant kelp). Animal-like cell membranes or plant-like cell walls envelope protist cells. In other protists, glassy silica-based shells or pellicles of interlocking protein strips encase the cells. The pellicle functions like a flexible coat of armor, preventing the protist from external damage without compromising its range of motion.

Metabolism

Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Protists that store energy by photosynthesis belong to a group of photoautotrophs and are characterized by the presence of chloroplasts. Other protists are heterotrophic and consume organic materials (such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest particles by a process called phagocytosis in which the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole. The vesicle containing the ingested particle, the phagosome, then fuses with a lysosome containing hydrolytic enzymes to produce a phagolysosome, which breaks down the food particle into small molecules that diffuse into the cytoplasm for use in cellular metabolism. Undigested remains ultimately exit the cell via exocytosis.

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Protist metabolism: The stages of phagocytosis include the engulfment of a food particle, the digestion of the particle using enzymes contained within a lysosome, and the expulsion of undigested materials from the cell.

Subtypes of heterotrophs, called saprobes, absorb nutrients from dead organisms or their organic wastes. Some protists function as mixotrophs, obtaining nutrition by photoautotrophic or heterotrophic routes, depending on whether sunlight or organic nutrients are available.

Motility

The majority of protists are motile, but different types of protists have evolved varied modes of movement. Protists such as euglena have one or more flagella, which they rotate or whip to generate movement. Paramecia are covered in rows of tiny cilia that they beat to swim through liquids. Other protists, such at amoebae, form cytoplasmic extensions called pseudopodia anywhere on the cell, anchor the pseudopodia to a surface, and pull themselves forward. Some protists can move toward or away from a stimulus; a movement referred to as taxis. Protists accomplish phototaxis, movement toward light, by coupling their locomotion strategy with a light-sensing organ.

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Different types of motility in protists: Protists use various methods for transportation. (a) A paramecium waves hair-like appendages called cilia. (b) An amoeba uses lobe-like pseudopodia to anchor itself to a solid surface and pull itself forward. (c) Euglena uses a whip-like tail called a flagellum.

Newly Discovered Eukaryotes

There are many new species to be discovered, including eukaryotic species.

Learning Objectives

Recognize Eukaryotic diversity

Key Takeaways

Key Points

  • We know only a fraction of the number of species out there, and most of the attention has been given to large macroscopic species, a true understanding of microscopic eukaryotic life is not known.
  • Even though mammals make up a small percentage of the species that are eukaryotes, several new mammalian species have been identified in the last decade.
  • As extinction is increasing, we may never know all the eukaryotes that share the world with us.

Key Terms

  • extant: Still alive; not extinct.
  • metagenomics: The study of genomes recovered from environmental samples; especially the differentiation of genomes from multiple organisms or individuals, either in a symbiotic relationship, or at a crime scene.

According to the Global Taxonomy Initiative and the European Distributed Institute of Taxonomy, the total number of species for some phyla may be much higher than what was known in 2010:10–30 million insects; (of some 0.9 million we know today) 5–10 million bacteria; 1.5 million fungi; of some 0.075 million we know today. The number of microbial species is not reliably known, but the Global Ocean Sampling Expedition dramatically increased the estimates of genetic diversity by identifying an enormous number of new genes from near-surface plankton samples at various marine locations.

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Known and Unknown Species: This graph shows how many species discovered (dark green) versus estimated species remaining to be discovered. This does not include many microscopic eukaryotic groups.

From these studies, it is apparent that less than 1% of all species that have been described have been studied beyond simply noting their existence. The vast majority of Earth’s species are microbial. Contemporary biodiversity is “firmly fixated on the visible world”. For example, microbial life is metabolically and environmentally more diverse than multicellular life (e.g., extremophile). On the tree of life, based on analyses of small-subunit ribosomal RNA, visible life consists of barely noticeable twigs. The inverse relationship of size and population recurs higher on the evolutionary ladder.

Due to the advent of mass sequencing tools, thousands of new viral species have been identified in metagenomics studies, while at the same time hundreds of new viral species have been found. On top of that, there have been numerous fungal species identified. However, as suggested above most of the attention is given to large species, which represent a very small portion of the new species identified Even with this in mind, since the beginning of this century, 5 marsupial species, 25 primate, 1 elephant, 1 sloth, 3 rabbit, several rodent species, at least 30 new bat species have been discovered. On top of that several subspecies have been found. Considering how large an elephant is, this should point out how little we know about the numbers of microscopic eukaryotes that are yet to be discovered.

Of course we may never truly identify many eukaryotic species, since the rate of extinction has increased. Many extant species may become extinct before they are described.