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Biology 110 - Basic Concepts and Biodiversity


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Protists I - Protists with Modified Mitochondria, Kingdoms Euglenozoa and Alveolata

Introduction and Learning Objectives

Figure 1.  Giardia lamblia, a protistan intestinal parasite.(Click to enlarge)

This tutorial will introduce protists, which are relatively simple eukaryotic organisms (such as Giardia lamblia, Figure 1). The taxonomy of this group is currently under extensive revision, therefore, no two textbooks present the same taxonomic scheme. Indeed, the emerging science of comparative genomics is almost daily revising the structure of the tree of life. For more on this emerging field, read this Discover Magazine blog post entitled "Festooning the Tree of Life".

This course uses a tree of life that has three domains (Archaea, Bacteria, and Eukarya; Figure 2). Recall, the non-mitochondrial/chloroplast DNA in a eukaryotic cell is located within the nucleus, which is surrounded by the nuclear envelope. Eukaryotic cells also possess extensive systems of intracellular membranes that provide elaborate internal compartmentalization. Additionally, eukaryotic cells usually have organelles that are specialized for different functions. In contrast, prokaryotic DNA is concentrated in the nucleoid region, which is analogous to the eukaryotic nucleus, but is not membrane-bound (discussed in Tutorial 4). Prokaryotes do not have mitochondria or chloroplasts, and they generally have internal membrane systems that are far less complex than those found in the eukaryotes.

This tutorial contains a number of links that have been included for your interest. The material in these Web sites need not be memorized unless the material is covered directly in the text of the tutorial.

By the end of this tutorial you should have a working knowledge of the following:

  • Different groups of protists including the protists with modified mitochondria and Kingdoms Euglenozoa and Alveolata
  • The role of protists in various mammalian diseases (e.g., giardiasis, trypanosomiasis, and malaria)
  • Dinoflagellates and their ecological roles in various habitats (e.g., coral reefs and red tides)

Performance Objectives (for both tutorials covering the Protists):

  • Describe the general characteristics of the protists
  • Summarize the basic classification of protists
  • Identify monophyletic, parpaphyletic and polyphyletic groups
  • For each taxonomic group of protists, identify the major characteristic(s) of that group and be able to discuss representatives that demonstrate the diversity of the group
  • Explain different ways in which protists impact humans, either directly or indirectly

Figure 2.  The three domain system for classifying life (click to enlarge)

What is a Protist?

Protists are, most often, fundamentally single-celled organisms. Like other eukaryotes, most have membrane-bound nuclei and organelles. Protists appear to be relatively simple organisms - only because most are unicellular (Figure 3). However, a closer inspection reveals that they really are surprisingly sophisticated. All of the essential metabolic functions that occur in multicellular organisms (e.g., respiration, photosynthesis, digestion, and excretion) also occur in protists. Moreover, many have sophisticated locomotion. The ubiquitous Euglena (Figure 4), found in most freshwater ponds, illustrates such protistan sophistication.

Figure 3.  The golden alga, Mallomonas sp.  (Click to enlarge)

Euglena possess (within a single cell): a flagellum for locomotion; an eyespot and light detector which, when used in concert, allows them to discern the direction of the most intense light (phototaxis); chloroplasts and mitochondria; a contractile vacuole for osmoregulation; a nucleus; and an extensive endomembrane system.

 Figure 4.  A drawing of a Euglena.  (Click to enlarge)

Protists are a metabolically and ecologically diverse group. Metabolically, they range from photosynthetic autotrophic species to heterotrophic species. They occupy diverse ecological habitats ranging from marine, to freshwater, to terrestrial. They have diverse relationships with other organisms, and are found free-living or as members of various symbioses.

With all of this diversity, protistan taxonomy is uncertain and the field is currently undergoing major changes. Some of these changes are confusing and reflect the uncertainty of how to best classify these organisms.


Some scientists still place all protists together into one kingdom, Protista. Although there are arguments for this classification scheme, in this course we will use a newer system that accommodates the great diversity of protists and recognizes many kingdoms within this group (Figure 5). Scientists working with protists generally agree that these organisms, as a group, are paraphyletic. While all eukaryotes arose from a single common ancestor (based on genetic sequence analyses and investigation of cellular components) and are a monophyletic group, the group “protists” does not contain all of its descendents because the fungi, plants and animals are recognized as separate kingdoms, making the “protists” paraphyletic.  The previous classification of protists into animal-like (Protozoa), plant-like (Protophyta) and fungus-like orgnanisms created many polyphyetic groups (members of the groups are descendants of different protist lineages).  Because it did not reflect the evolutionary history of the group, that classification system has been discarded but you will occasionally see  the terms "protozoa" or "protist" used.

For the sake of convenience we will use the term "protist," but keep in mind that this is not a taxonomic term; rather, "protist" describes a diverse group of mostly single-celled eukaryotes.

Figure 5. The classification of Eukaryotes. (Click to enlarge)

In this tutorial, you will learn about two of the five kingdoms that have been best characterized: Euglenozoa and Alveolata.  You will also learn about the protists with modified mitochondria.  In the next tutorial, two more kingdoms will be examined: Stramenopila and Chlorophyta. There are some protists that do not fit into these kingdoms, and more kingdoms, and the relationships among them, are emerging as work on these groups progresses.


Pelomyxa is a very simple eukaryote

The protist Pelomxya (Figure 6), gives us insights into how simple a eukaryotic cell can be, and what very early eukaryotes may have looked like. It is a eukaryote because it has a membrane bound nucleus with linear chromosomes.  However, it has no endoplasmic reticulum, no Golgi, and no mitochondria.  It depends upon endosymbiotic bacteria (and sometimes archaea!) that live within its cytoplasm. If those bacteria are killed by antibiotics, the Pelomyxa will die.  Based upon recent molecular data, it appears that Pelomyxa descended from protists that had organelles but lost them. Pelomyxa lives in the mud in the bottom of freshwater ponds and streams.  

Protists with Modified Mitochondria

Two groups of protists - the diplomonads (Figure 7) and the parabasalids (Figure 8) have highly modified mitochondria. The evidence suggests that each group is monophyletic but what is less clear is how closely related these two groups are to each other.


Figure 7.  A diplomonad.  (Click to enlarge) Giardia lamblia, an intestinal parasite.

Figure 8.  A Parabasalid: Trichomonas vaginalis. This specimen was obtained from an in vitro culture.

The Diplomonads

The diplomonads have modified mitochondria (called mitosomes) that lack functional electron transport chains and thus are unable to perform cellular respiration so they derive their energy from pathways such as glycolysis. They also lack Golgi, but always have flagella. These organisms are found in anaerobic environments and are often parasites.

The diplomonad Giardia, is an intestinal parasite responsible for the disease giardiasis or "beaver fever," which is generally transmitted via contaminated drinking water. Giardia attaches to the intestinal epithelium, or lining, in humans and other mammals (e.g., dogs, cats, bears, and beavers), creating severe diarrhea and intestinal cramps (Figure 9 and 10). Unlike bacterial infections, in which a large number of organisms must be ingested to cause illness, a few Giardia individuals can cause a severe case of giardiasis. The parasite is endemic to many wilderness areas; infection can be prevented by treating the water either with a biofilter or with chemicals such as bleach. While it is a decidedly unpleasant disease to have, giardiasis is fairly easily treated with drugs.


Figure 9.  Giardia intestinalis in culture. (Click to enlarge)  In these preparations, the flagella (four pairs per cell) are clearly visible.

Figure 10. Cysts of Giardia intestinalis from a human patient. (Click to enlarge)  Note that each Giardia cell has two nuclei, as do all diplomonads.

The Parabasalids

The parabasalids are anaerobes that lack functional mitochondria but some species contain a structure known as a hydrogenosome that may be a degenerate mitochondrion;they do have functional Golgi. They also have flagella. Perhaps the best known parabasalids are in the genus Trychomonas (for example, T. vaginalis (Figure 8) is a sexually transmitted parasite that infects millions of people a year) and are parasites of animals. However, another important group of parabasalids are endosymbionts of insects and live in these animals’ guts. For example, members of the genus Trychonympha are important symbionts in termite guts (Figure 11); the Trychonympha contain endosymbiotic bacteria that help them break down cellulose in the termite gut. This allows termites to consume wood (which can be a problem if they choose to eat your wooden house).

Figure 11. A Trychonympha sp. that lives in the guts of termites  (Click to enlarge)  

A Real Life Example:  Studying a parabasalid to improve our energy infrastructure

Termites are an economically important insect species because of the damage they can do to wooden structures such as houses. Termites are able to use cellulose-containing materials (such as wood and paper) as a food source because their hindguts contain a complex community of both prokaryotic and eukaryotic symbionts. Many of these symbionts, such as the protist Trichonympha (a member of the trichomonads which lack functional mitochondria) and their bacterial symbionts, produce the enzyme cellulase which hydrolyzes cellulose to glucose; this glucose can then be fermented to ethanol.

Cellulose is the most abundant renewable resource on earth. As a result, there is current interest in developing efficient methods for turning cellulose into ethanol fuels. Currently, large scale commercial ethanol production utilizes corn as the starting material. However, there are some studies that have questioned the long-term sustainability of using corn for this purpose (i.e., when all costs associated with the production of ethanol from corn are totaled, and current farm subsidies are subtracted, there may be no value in this method of producing ethanol).  Nobel Laureate (and former Secretary of Energy) Steven Chu has suggested that the termite may help us improve the efficiency of ethanol production:

“This is where the termite guts come in. A billion years of evolution have produced a highly efficient factory for turning cellulose into ethanol, unlike anything which humans can yet design”.

The Chu lab has worked on genetically engineering the organisms in the termite gut to produce abundant supplies of ethanol.

  • What characteristic of Trichonympha allows us to classify them as parabasalids?
  • What is the name of the process that produces ethanol from glucose?
  • Briefly describe the structure of cellulose.




Kingdom Euglenozoa

Although the euglenozoans are monophyletic (derived from a single ancestor), they are a diverse group in terms of their feeding strategies. Kingdom Euglenozoa includes heterotrophs, such as Trypanosoma, and autotrophs, such as Euglena (Figure 12). This kingdom can be divided into two groups. The first consists of Euglena and its relatives, collectively called the euglenoids. These organisms are primarily photosynthetic. All euglenoids have flagella (structurally different from those of prokaryotes). Click here to see movies of Euglena at the Website called "Molecular Expressions."

Figure 12. A Euglena sp.  (Click to enlarge) 

The second group of euglenozoans is the kinetoplastids, which includes Trypanosoma and its relatives, all of whom have one large mitochondrion and an organelle called a kinetoplast, which stores extranuclear DNA. All kinetoplastids live in symbiosis with host organisms, and a number of them are pathogenic. For example, the disease African trypanosomiasis, or African sleeping sickness, is caused by euglenozoans from the genus Trypanosoma (Figure 13). African Trypanosoma species are transmitted between mammalian hosts by the tsetse fly, a biting insect that transfers the parasite from the blood of infected individuals to the blood of uninfected hosts. The symptoms of African sleeping sickness include fatigue and confusion, which results after Trypanosoma invades the central nervous system - using this CDC link, which body fluid is tested to determine if the parasite is present in the CNS? . This disease, although fatal if left unchecked, can be treated.

Figure 13.  Trypanosoma brucei (blue) and red blood cells (gray) of an individual infected with African sleeping sickness. (Click to enlarge)

Another parasite from this same genus causes Chagas disease, or American trypanosomiasis (Figure 14), which is transmitted by insects known as "kissing bugs." Chagas disease, which occurs primarily in rural areas of Central and South America, affects between 8 and 11 million people and kills nearly 40,000 every year. It tends to be a chronic infection that causes acute symptoms (e.g., gastrointestinal discomfort and heart enlargement or other cardiac problems) between 10 and 20 years after infection.

Figure 14. Trypanosoma cruzi (purple) among human red blood cells (beige). (Click to enlarge)  Trypanosoma cruzi is responsible for Chagas disease.

There is some speculation that the debilitating fatigue and gastrointestinal distress that plagued Charles Darwin for the better part of his life after his return to England from South America was actually due to a chronic infection of Chagas disease.
Preventive measures for both African sleeping sickness and Chagas disease are largely focused on vector control, which ranges from insecticide-treated bednets (ITNs) to the "sterile insect technique", " Read this article to find out what the sterile insect technique is.  How do they ensure that these insects will be sterile in a natural environment?







Introduction to Kingdom Alveolata

The kingdom Alveolata is another diverse group. It includes some of the most familiar and ecologically interesting protists in existence, including those that build coral reefs (Figure 15), the organism that causes malaria (Figure 16), and the algae that poison fish during red tide events (Figure 17). This group is monophyletic and recognizable by their alveoli (small cavities enclosed in membranes that hug the internal cell surface). There are three distinct groups of alveolates: dinoflagellates, apicomplexans, and ciliates.  The remainder of this tutorial will concentrate on the dinoflagellates and apicomplexans.


Figure 15. A dinoflagellate. (Click to enlarge) Peridinium sp. 

Figure 16.  An apicomplexan.  Plasmodium falciparum.

Figure 17. A ciliate.  (Click to enlarge) Stentor sp.

Kingdom Alveolata: Dinoflagellates

Dinoflagellates usually have distinct shapes due to "frames" of cellulose within their cell walls. Their cell surface is generally ridged with perpendicular grooves that house a pair of flagella (Figure 18). These flagella, the defining characteristic of this group, beat within their grooves and cause dinoflagellates to rotate as they move forward. The word dinoflagellate is derived from the Greek word dinos, which means "rotation" or "whirling," and the Latin flagellum, which means "whip."

Many dinoflagellates are photosynthetic; accordingly, they comprise a significant proportion of the phytoplankton that floats near the surface of the ocean, making them a critical component of the aquatic food web (Figure 19). Phytoplankton are an essential food resource for many other organisms, ranging from heterotrophic protists to baleen whales and many other organisms in between (most of whom serve as food themselves for creatures at higher trophic levels).

Figure 18.  A dinoflagellate. (Click to enlarge) Ceratium tripos.

Many dinoflagellates are photosynthetic; accordingly, they comprise a significant proportion of the phytoplankton that floats near the surface of the ocean, making them a critical component of the aquatic food web (Figure 19). Phytoplankton are an essential food resource for many other organisms, ranging from heterotrophic protists to baleen whales and many other organisms in between (most of whom serve as food themselves for creatures at higher trophic levels).

Figure 19.  Food web for an aquatic ecosystem (

Not all dinoflagellates are photosynthetic; many are heterotrophic. Some of these heterotrophs exploit chloroplasts from photosynthetic protists, becoming autotrophic themselves for a time. Some dinoflagellates live in symbiosis with different species, as parasites in some cases and as mutualists in others.


Some dinoflagellates, such as those in the genus Noctiluca, have the ability to bioluminesce (make their own light). This is accomplished with the compound luciferin, which is the same chemical that makes fireflies glow. Noctiluca floats just under the surface of the ocean, and when individuals number in the millions they can produce spectacular glowing tides (Figure 20). The blue in the image is the visible glow that is triggered by the tumbling dinoflagellates as the water is disrupted. If you walk along the tide line of a beach with these dinoflagellates, your footprints actually glow with each step when your foot disturbs these bioluminescent protists. How bioluminescence evolved is not completely understood. The Burglar Alarm theory posits that the bioluminescent glow attracts predators of dinoflagellate predators and this allows the glowing protist to escape predation (Figure 21).

Figure 20.  A dinoflagellate. (Click to enlarge) Noctiluca scintillans is one dinoflagellate responsible for red tides.

Figure 21.  A bioluminescent algal bloom. (Click to enlarge)

This image shows a bloom of bioluminescent Noctiluca scintillans

Dinoflagellates and Coral Reefs

One of the mutualistic associations formed by dinoflagellates is their symbiotic relationship with reef-building cnidarians, animals in the same phylum as sea anemones and jellyfish (Figure 22). Corals engulf dinoflagellates but do not digest them; rather, these dinoflagellates, called zooxanthellae, live out their lives within the tissues of corals (Figure 23). How do you think each of the partners in this mutualistic symbiosis benefit? 


Figure 22.  Individual cnidarian polyps (coral-building organisms). (Click to enlarge)

Figure 23.  Zooxanthellae within a coral polyp (Click to enlarge)

Coral reefs are actually composed of the exoskeletons (secreted calcium carbonate shells) from countless generations of organisms, each of which anchored itself onto the remains of the previous generation, secreting more calcium carbonate and building up the reef incrementally over time.
While some corals are capable of existing without symbiotic protists, they do not thrive and the rate of calcium carbonate deposition (reef-building) is far slower when dinoflagellates are absent. As tiny as dinoflagellates are, the energy they provide helps the corals to build reefs that are thousands of miles long.

Furthermore, reefs are complex vital ecosystems that support many life forms that simply would not exist if reefs disappeared; therefore, a great many organisms are indirectly dependent on the activity of dinoflagellates.

Recently many reefs have begun to suffer, becoming dramatically bleached in appearance as the corals lose their zooxanthellae. There have been a number of hypotheses advanced to explain this phenomenon (e.g., pollution, an increase in ultraviolet light due to the widening hole in the ozone, and global temperature changes); all of these factors can be traced back to the impact of humans on the environment. Others suggest that natural weather fluctuations or disease outbreaks may be responsible. Whatever the ultimate cause, loss of symbiotic dinoflagellates appears to be the immediate source for the bleaching. For more information on coral bleaching check out the NOAA (National Oceanic and Atmospheric Administration) Coral Reef Site, and the Australian Institute of Marine Science.  Using the map on the NOAA Coral Reef Watch Site, which ocean is currently experiencing the highest Alert level of coral bleaching?.


Dinoflagellates and Red Tide

Dinoflagellates are the organisms responsible for red tide events, or "harmful algal blooms" (HABs). Blooms (population explosions) of dinoflagellates are called "red tides" because dinoflagellates can reach such high densities that they actually change the color of the water in which they reside. Depending on the pigments present in these dinoflagellates, these tides will appear brown, red, orange, or yellow (Figure 24).

Figure 24. A red tide in Hong Kong.  (Click to enlarge)

A number of dinoflagellate species release toxins into the water, killing many aquatic animals during major algal blooms and poisoning others with sublethal doses of toxins (Figure 25). The primary function of these compounds is probably defensive, warding off or poisoning grazers, and perhaps preventing competing algal species from gaining a foothold in monospecific mats of plankton (minute animal and plant life in the ocean).

A recent study suggests that these toxins, known as brevetoxins, can be aerosolized during HAB events, increasing the incidence of respiratory infections among inland populations by 54%.

In any case, filter feeders, such as shellfish, are particularly vulnerable to brevetoxins because they actively ingest plankton. In turn, heterotrophs (including humans) that eat poisoned animals are often themselves unintended victims of the dinoflagellates' defensive chemicals, contracting such conditions as paralytic shellfish poisoning. The compounds involved are neurotoxins, poisons that attack the central nervous system, so they are particularly nasty, producing symptoms such as delirium and respiratory paralysis.  Using the information in the CDC web page, how many cases of poisoning by marine toxins are reported in the US each year?

Figure 25.  Alexandrium sp.  (Click to enlarge) A red tide organism.

One red tide organism, Pfiesteria (Figure 26), is unusual in that it uses toxins specifically to kill fish, stunning them and then feeding on their tissues (or on other protists that thrive on decaying fish). Pfiesteria also produce some of the most ecologically severe red tides, sometimes killing enormous numbers of fish. It is not clear how Pfiesteria affect humans, but there does seem to be considerable evidence that people exposed to its toxin by physical contact with affected fish or water containing Pfiesteria suffer various symptoms (e.g., skin lesions and loss of cognitive function).

Figure 26.  Pfiesteria sp. (Click to enlarge)

HABs seem to be on the rise. Scientists believe that the enrichment of oceans and estuarine waters from fertilizer runoff has created an aquatic environment that favors dinoflagellate blooms. Research is underway to learn more about the causes of HABs, with the ultimate goal of designing viable control measures. There is a very obvious mistake in the title of this NOAA page that offers a more thorough explanation of HAB causes and control strategies.  Do you know what it is?


Can protists really be seen from space? They can if they cause red tides. NOAA, the National Oceanic and Atmospheric Administration, sponsors many programs to monitor HABs using satellite imagery. Figure 27 is from a study that is focused on the dinoflagellate Gymnodinium breve, which causes HABs in the Gulf of Mexico.

Figure 27.  A satellite image from NOAA showing hot spots (in red) of Gymnodinium breve. (Click to enlarge)

Kingdom Alveolata: Apicomplexans

Apicomplexans are parasites, specialized for living and reproducing within the tissues of animals. The apical complex is a cluster of microtubules and organelles located in the apex of cells that are in the infectious stage. This structure's function is to facilitate penetration of host cells. A number of apicomplexans require more than one host to complete their complicated life cycles. The infamous Plasmodium (Figure 28), which causes malaria in humans and other animals, is an apicomplexan transmitted by mosquitoes.

Figure 28. Plasmodium falciparum, an apicomplexan.

More people are killed each year by malaria than by any other transmissible disease (besides tuberculosis); over one million people die each year from malaria (of approximately 515,000,000 infections every year), with the overwhelming majority of cases occurring in sub-Saharan Africa (and many others in Southeast Asia and South America). What's more, malaria can strike a person multiple times per year, contributing to a major deficit in productivity, depriving families of income, and plunging many into deeper poverty. 


Many apicomplexan life cycles are quite complex, and Plasmodium is no exception (Figure 29).  As you can see, there are many stages in the life cycles of this parasite, and each stage infects a different host or tissue within the host. You do not need to know the details of this life cycle, but you should understand the implications of this complexity in the attempt to develop a cure for malaria.

Figure 29. The life history of Plasmodium, the apicomplexan that causes malaria. (Click to enlarge)

If you are interested in parasitic disease organisms, check out the CDC Disease Database for thorough, reliable information, along with some worthwhile images. 






The protists are comprised of very diverse organisms that are polyphyletic in origin. Earlier taxonomic schemes that grouped all of these organisms into a single kingdom were not very informative because they were not based on the evolutionary relationships between different protistan groups. The revised classification scheme presented here is considered superior because it does take into account these evolutionary relationships.

As you learned, not all eukaryotes have mitochondria. Keep in mind that their lifestyle (as microsymbionts) does not require these organelles because they are quite successful living in the way that they do (although, sometimes at the expense of their hosts).

Members of the kingdom Euglenozoa do have mitochondria, but are a diverse group in terms of structure. All euglenoids have a flagellum, whereas the kinetoplastids have a kinetoplast. The euglenoids are typically free-living (and can be photoautotrophic), whereas the kinetoplastids are all microsymbionts (some, like the trypanosomes, are pathogenic).

Members of Kingdom Alveolata are even more diverse. They include the dinoflagellates that are involved in such diverse activities as coral reef building and that cause various forms of red tide. They play a major role in the ecology of ocean communities because they comprise a significant portion of the phytoplankton that forms the basis of many aquatic food webs.

The apicomplexans all form parasitic symbioses, therefore, they have a major impact on other life. The causative agent of malaria is caused by Plasmodium. More people are killed each year by malaria than by any other transmissible disease (besides tuberculosis). Keep in mind the importance of understanding a pathogen's life cycle when public health decisions need to be made.



After reading this tutorial, you should have a working knowledge of the following terms:

  • alveoli
  • alveolate
  • apical complex
  • apicomplexan
  • bioluminescence
  • dinoflagellate
  • diplomonad
  • euglenoid
  • euglenozoan
  • exoskeleton
  • kinetoplast
  • kinetoplastid
  • monophyletic
  • parabasalids
  • phytoplankton
  • plankton
  • polyphyletic
  • protist
  • trichomonad
  • zooxanthellae

 Questions?  Send your instructor a message through ANGEL!



Added by Denise Woodward , last edited by Denise Woodward on Aug 05, 2015 15:01