Protist doc
Definition of Protist
**General Definition: **
Protists are recognized as a diverse group of organisms that do not fit into the traditional kingdoms: Animalia, Plantae, or Fungi.
Features:
Mostly aquatic habitat.
Eukaryotic cells, distinguished from prokaryotes.
Characterized by diverse body forms, methods of reproduction, nutritional modes, and lifestyles.
Protist Types
Inclusion of Various Forms:
Algae (e.g., green and red algae).
Water molds (e.g., Pythium).
Slime molds (e.g., Physarum).
Protozoa (e.g., Amoeba, Paramecium).
Cellular Organization:
Can be unicellular (e.g., Chlamydomonas), colonial (e.g., Volvox), or multicellular (e.g., Spirogyra).
Diverse Modes of Locomotion in Protists
Verbal Examples of locomotion:
Amoeba: Uses pseudopodia (temporary projections of cytoplasm) to move.
Euglena: Propelled by flagella (whip-like structures).
Paramecium: Moves via cilia (short hair-like structures).
Systematics of Eukaryotes
Current Classification Changes:
Significant re-evaluations of eukaryotic systematics show that protists form a paraphyletic group.
The term Protista is no longer valid as a strict kingdom.
Phylogenetic Placement
Prokaryotes:
Domain: Bacteria and Archaea
Eukaryotes:
Domain: Eukarya
Kingdoms include: Animalia, Fungi, Plantae, and the informal grouping of Protista.
Eukaryotic Diversity
Domain Eukarya:
Encompasses a broad range of organism sizes from unicellular (similar to bacteria) to large multicellular organisms such as sequoias and blue whales.
Unifying Characteristics of Eukaryotes:
Generally larger than prokaryotic cells.
More complex with a variety of organelles and an extensive cytoskeleton.
Possession of a nuclear envelope.
Multicellularity evolved multiple times within this group.
Capable of both asexual and sexual reproduction.
examples of Eukaryotic Cells
Eukaryotic Cell Structure Comparison:
Typical components include a nucleus, endoplasmic reticulum, Golgi apparatus.
Advantages of eukaryotic cells are their complexity and functional specialization.
Significance of Protists
Ecological and Health Impacts:
Plays critical roles in ecosystems, particularly aquatic environments.
Understanding of protists aids in researching plant, fungal, and animal evolution.
Certain protists can cause diseases in crops (e.g., Irish Potato Famine caused by Phytophthora infestans, a water mold).
Health Risks from Protists:
Malaria: caused by Plasmodium (e.g., P. falciparum, P. vivax), affects over 3.4 billion people.
Toxoplasmosis: caused by Toxoplasma gondii, significant for immunocompromised patients and newborns.
Harmful Algal Blooms:
Caused by toxin-releasing dinoflagellates, accumulate in clams causing human poisoning.
Importance in Aquatic Ecosystems
Oxygen Production:
Photosynthetic protists are primary producers and are crucial for underwater food webs.
They contribute to global carbon fixation - marine protists fix nearly half of the Earth's CO2.
Plankton Contribution:
Diatoms and small organisms form the base of many aquatic ecosystems.
Algal Blooms and Mitigation Strategies
Red Tides:
Rapid population growth of toxic dinoflagellates, such as Karenia brevis, leads to environmental and health issues.
Clay Utilization in Red Tide Control:
Research indicates that dispersing tiny clay particles can mitigate algal blooms effectively.
Mechanism of action includes flocculation where clay particles bind to dinoflagellates, aiding in their precipitation and neutralization of toxins.
Role of Protists in Food Webs
Trophic Relationships:
Protists are fundamental in aquatic food webs as primary producers that convert energy from sunlight into biomass.
Carbon Sequestration
Function as Carbon Sinks:
Long-lived reservoirs of carbon, particularly in sedimentary formations from protists with CaCO3 shells.
Accumulation leading to petroleum reserves from organic matter deposits at ocean bottoms.
Study of Protists
Evolutionary Patterns:
Evolutionary relationships among protists display extensive divergence with no single shared characteristic distinguishing them from other groups.
DNA analysis has begun to clarify relationships in their evolutionary lineage.
Major Groups of Eukaryotes and their Distinctions
Eukaryotic Lineage Grouping:
Grouping based on cell structure, distinctive organelles, and molecular characteristics:
Excavates (e.g., Diplomonads, Euglenoids).
Chromalveolates (e.g., Alveolates, Stramenopiles).
Rhizarians (e.g., Foraminifera).
Archaeplastids (e.g., Red and Green algae).
Unikonts (e.g., Amoebozoa, Opisthokonts).
Molecular Phylogenies in Protists
Phylogenetic Insights:
Morphological and genetic data support monophyletic classifications for the identified eukaryotic groups.
Hypotheses on the origin suggest a divergence between the Unikonta and Bikonta groups, with further subdivisions outlined in phylogenetic diagrams.
Summary of Protist Types and Characteristics
Table of Clades in Protists:
Excavates:
Atypical mitochondria, multiple flagella (Diplomonads, Euglenoids);
Chromalveolates:
Result of secondary endosymbiosis (Dinoflagellates, Stramenopiles);
Rhizarians:
Amoeboid cells typically with hard tests/shells;
Archaeplastids:
Land plants and algae with two membranes around plastids;
Unikonts:
Includes animals and fungi with unique genetic characteristics.
Major Protist Groups
Diplomonads
Excavates
Euglenoids
Dinoflagellates
Apicomplexans
Ciliates
Chromalveolates
Alveolates
Water molds
Diatoms
Stramenopiles
Brown algae
Golden algae
Ancestral eukaryote
Forams
Rhizarians
Actinopods
Red algae
Archaeplastids
Green algae
Land plants
Amoebas
Plasmodial slime molds
Cellular slime molds
Unikonts
Opisthokonts
Fungi
Choanoflagellates
Animals
Eukaryotic Group Distinctions
Prokaryotes: Separate lineage from eukaryotes
Unikonta:
One-tailed lineage containing more fungi-like groups
Includes Kingdoms Fungi and Animalia
Bikonta:
Two-tailed lineage
Major Lineages of Protists
Seven major Eukarya lineages each characterized by morphological distinctiveness
Distinctive cell structures led to diversification in lifestyles
Features may also evolve independently in various lineages, illustrating convergent evolution
Amoebozoa
Lobose Amoebae:
Lack cell walls
Engulf food for nourishment via amoeboid movement using lobe-like pseudopodia
Exhibits cytoplasmic streaming
Highly abundant in aquatic habitats and wet soils
Some species are internal parasites in humans and animals
Relevance: Influences nutrient cycling through microorganism feeding
Example: Dictyostelium discoideum as a model organism in cell biology
Slime Molds (Mycetozoans)
Previously classified as fungi
DNA reveals resemblances due to convergent evolution rather than a common ancestry
Divided into two main lineages:
Plasmodial slime molds
Cellular slime molds
Life Cycle of Plasmodial Slime Molds
At the feeding stage, forms a mass called a plasmodium:
Not multicellular; undivided by plasma membranes
Contains many diploid nuclei
Extends pseudopodia for food engulfment via phagocytosis
Does not have chitinous cell walls
Life Cycle of Cellular Slime Molds
Forms multicellular aggregates with cells separated by membranes
Individual cells feed, but they can also aggregate together to migrate and form a fruiting body
Dictyostelium discoideum: significant for understanding evolution of multicellularity
Excavata Group
Characterized by an excavated feeding groove on one side
Some may be mitochondria-less, though ancestors likely possessed them
Some retain vestigial mitochondria and others show mitochondrial genetic material
Predominantly unicellular heterotrophs
Locomotion via whiplike flagella
Major Groups within Excavata
Parabasalids:
Possess reduced mitochondria called hydrogenosomes for energy generation
Includes Trichomonas vaginalis, a pathogen causing yeast infections
Diplomonads:
Deep oral groove direct feeding behavior
Contain mitochondria known as mitosomes; energy derived from anaerobic processes
Characterized by two nuclei and multiple flagella
Example: Giardia intestinalis, a common intestinal pathogen
Lifecycle of Giardia
Cyst forms when contaminated:
Ingestion of Giardia cyst through contaminated water, food, or contact
Transforms into trophozoite in the small intestine, where it multiplies and absorbs nutrients
Cysts excreted, existing in the environment for extended periods
Euglenozoans
Highly diverse clade consisting of:
Predatory heterotrophs
Photosynthetic autotrophs
Mixotrophs
Parasites
Key distinction: spiral or crystalline structure present in flagella
Euglenids
Can display dual flagella emerging from a pocket at one end
Exhibit both autotrophic and heterotrophic capabilities
Contains structures like eyespot facilitating light detection
Kinetoplastids
Many are obligate parasites, requiring host organisms for survival
Utilize flagella and an undulating membrane for movement
Notable examples include trypanosomes
Phylogenetic Analyses
A comprehensive diagram illustrates seven major lineages of eukaryotes with associated key subgroups:
Amoebozoa: Lobose amoebae, cellular slime molds, plasmodial slime molds
Opisthokonta: Fungi and Animals
Excavata: Parabasalids, Diplomonads, Euglenids
Plantae: Glaucophytes, Red algae, Green algae, and Land plants
Rhizaria: Foraminiferans, Actinopods, Chlorarachniophytes
Alveolata: Ciliates, Dinoflagellates, Apicomplexans
Stramenopila: Water molds, Diatoms, Brown algae
Overview of Plantae (Archaeplastids)
Monophyletic group: Member organisms share a single common ancestor.
Origin: Descended from a common ancestor that engulfed a cyanobacterium through the process of endosymbiosis.
Subgroups: There are four main subgroups of plantae:
Red Algae
Green Algae
Land Plants
Glaucophyte Algae
Classification of Eukaryotes
Eukaryotic Domain: The major groups of eukaryotes include:
Amoebozoa: Includes lobose amoebae, cellular slime molds, and plasmodial slime molds.
Opisthokonta: Comprising fungi, choanoflagellates, and animals.
Excavata: Includes parabasalids and diplomonads.
Unikonta: This group includes euglenids and kinetoplastids.
Plantae: Subgroups include glaucophyte algae, red algae, green algae, and land plants.
Rhizaria: Contains actinopods, foraminiferans, and chlorarachniophytes.
Alveolata: Comprises ciliates, dinoflagellates, and apicomplexans.
Stramenopila: Includes water molds, diatoms, and brown algae.
Diversity of Algae
General Characteristics of Algae
Forms: Algae can exist in various forms including unicellular, colonial, or multicellular.
Composition:
Contain chloroplasts for photosynthesis.
Cell walls are primarily composed of cellulose.
Movement: Algae produce flagellated reproductive cells.
Reproduction: Both asexual and sexual reproduction are observed, with some demonstrating alternation of generations.
Ecological Role: Algae are significant as primary producers in most ecosystems. Additionally, some red algae contribute to coral reef development, and agar is derived from their cell walls.
Red Algae
Description: Commonly recognized as seaweeds, they display a reddish color due to the pigment phycoerythrin, which masks chlorophyll.
Color Range: Color can vary from greenish-red (found in shallow water) to dark red or almost black (found in deep water).
Structure: Usually multicellular and considered the largest seaweeds; they are the most abundant large algae in tropical coastal waters.
Example: Nori, a species of red algae, belongs to the genus Pyropia.
Why Aren’t Seaweeds Considered Plants?
Root Structures: Seaweeds lack true roots; they may have structures that anchor them to the substrate but do not absorb nutrients.
Nutrient Absorption: They absorb nutrients from surrounding water rather than through a vascular system.
Reproductive Simplicity: They possess a simple reproductive system that utilizes spores.
Green Algae
Coloration: Green algae are predominantly green due to chloroplasts.
Relationship: Land plants are believed to have evolved from green algae.
Forms: These can also be unicellular or multicellular, giving rise to examples like Ulva (sea lettuce) and Caulerpa (an intertidal chlorophyte).
Benefits of Green Algae
Nutritional Value: Ulva is rich in proteins, vitamins, trace minerals, and dietary fibers, serving as:
A main ingredient in dishes.
A seasoning or a substitute for other foods.
Growth Rate: Green algae demonstrate rapid growth, efficiently using space compared to land plants.
Environmental Impact: They offer eco-friendly alternatives in aquaculture and agriculture, thereby reducing environmental impact.
Biomaterial Applications: Useful as plant biostimulants, packaging materials, and in biorefineries.
Resource Efficiency: Require no external inputs such as fertilizers, pesticides, or arable land.
Glaucophyte Algae
Characteristics: Comprising a small group of 14-26 unicellular species, inhabiting aquatic or moist terrestrial environments.
Scientific Importance: They are considered a model system for studying chloroplast evolution.
Reproduction: Primarily reproduce asexually.
Rhizaria
Morphology: These are unicellular, lack cell walls, and may have elaborate shell-like tests or coverings.
Locomotion: They exhibit amoeboid locomotion characterized by long, slender pseudopodia.
Reproductive Strategy: Generally reproduce asexually but sexual reproduction can occur, involving meiosis that produces haploid gametes.
Ecological Relevance:
Shells of dead foraminiferans contribute to sedimentation on the ocean floor, leading to limestone formations.
Presence of certain shell types can assist in geological dating during petroleum exploration.
Characteristics of Rhizaria
Amoeboid Nature: Many species are classified as amoebas with distinct threadlike pseudopodia.
Diversity: Includes radiolarians, foraminiferans, and others, most of which are heterotrophic, with few photosynthetic species.
Radiolarians
Habitat: Primarily marine organisms.
Structure: Have symmetrical internal skeletons made usually of silica.
Feeding Mechanism: Use pseudopodia extended through shell pores to engulf microorganisms via phagocytosis.
Foraminiferans (Forams)
Description: Characterized by porous, multichambered tests made of CaCO3.
Locomotion: Pseudopodia extend through pores in the test, allowing for movement and phagocytosis.
Ecological Role: Most are benthic; some exist in planktonic forms and are predominantly marine, with some hosting endosymbiotic algae.
Morphological Details of Foraminiferans
Common structure includes:
Test: Made up of multiple chambers;
Pseudopodia: Extend through the test allowing for locomotion and food capture.
Cellular Components: Include a nucleus, digestive vacuoles, and various organelles crucial for metabolism and growth.
Alveolata
Structural Features: Characterized by flattened, membrane-bound vesicles known as alveoli that support their plasma membranes.
Diversity: Although mostly unicellular, they exhibit varied morphology and lifestyle.
Bioluminescence: Some species are noted for their ability to emit light via enzyme-catalyzed reactions.
Ecological Roles:
Includes free-living and parasitic species with significant ecological impacts.
Reproductive Strategies: Exhibits both asexual and sexual reproduction methods, comprising multiple life cycles within subgroups.
Key Groups within Alveolata
Ciliates: Move using cilia and are known for their complex cellular structure.
Dinoflagellates: Photosynthetic organisms that can be bioluminescent; some are known for causing red tides.
Apicomplexans: Notable for being parasites; responsible for various diseases in humans and animals.
Classification of Protists
Protists represent a diverse range of organisms classified into several groups, excluding the fungi, animals, and land plants, which are categorized separately within the domain Eukaryota.
Major Lineages of Eukaryotes
Amobozoa
Lobose amoebae
Cellular slime molds
Plasmodial slime molds
Opisthokonta
Includes Fungi, Choanoflagellates, and all animals
Excavata
Parabasalids, Diplomonads, Euglenids, Kinetoplastids
Plantae
Glaucophyte algae, Red algae, Green algae
Green plants leading to land plants
Rhizaria
Actinopods, Foraminiferans, Chlorarachniophytes
Bikonta
Includes Alveolata and Stramenopila
Alveolata: Ciliates, Dinoflagellates, Apicomplexans
Stramenopila: Water molds, Diatoms, Brown algae
Alveolata
Alveolata are characterized by membrane-bound vesicles known as alveoli, which are located just beneath their plasma membranes.
General Characteristics:
Unicellular but have diverse morphologies and lifestyles.
Some species are capable of bioluminescence, emitting light through enzyme-catalyzed reactions.
They can be free-living or parasitic.
Diversity within Alveolata
Includes three major subgroups: Ciliates, Dinoflagellates, and Apicomplexans.
Reproductive strategies include both asexual and sexual processes.
Movement: Ciliates use cilia, Dinoflagellates utilize flagella, and some Apicomplexans exhibit amoeboid motion.
Dinoflagellates
Morphological Features:
Have two flagella for movement.
Cells are reinforced with cellulose plates.
Habitat: Primarily marine and aquatic environments; abundant in phytoplankton.
Nutritional Groups: Some are phototrophs, others mixotrophs or heterotrophs.
Ecological Impact: Some species produce toxins that can lead to harmful algal blooms, commonly known as red tides.
Bioluminescence in Dinoflagellates
Behavioral Responses:
Dinoflagellates exhibit bioluminescence when disturbed, which has a predatory escape function.
Sequence of Events:
The dinoflagellate flashes when captured by a copepod.
This flash triggers the copepod to jump, likely avoiding predation.
The disturbance creates a fluid motion that attracts larger predators.
Symbiotic Relationships
Some dinoflagellates, known as zooxanthellae, live symbiotically with coral polyps, providing them with nutrients through photosynthesis and contributing to the structural integrity of coral reefs.
Coral Bleaching
Symbiotic Relationship Breakdown:
Coral and zooxanthellae maintain a mutualistic relationship.
Stressors, such as changes in ocean temperature (primarily due to climate change), lead to the expulsion of zooxanthellae from coral tissues.
This results in coral appearing white or bleached and makes them susceptible to disease due to lack of food.
Causes of Bleaching:
Increased ocean temperatures.
Runoff and pollution from storms diluting ocean waters.
Overexposure to sunlight during high-temperature periods.
Extreme low tides exposing corals to the air.
Apicomplexans
Characteristics:
Nature: They are parasitic, infecting humans and animals.
Life Cycle: Spread through infectious cells known as sporozoites.
Morphological Feature: Have an apical complex, a structure with organelles that facilitate penetration into host cells.
Reproductive Cycles: Both sexual and asexual reproduction methods may occur, often requiring multiple hosts to complete their life cycle.
Example: Plasmodium, the causative agent of malaria, goes through complex life stages and requires both humans and mosquitoes to complete its life cycle.
Ciliates
General Information:
Ciliates are characterized by their use of cilia for movement and feeding.
They generally have a dual nuclei system consisting of a macronucleus and one or more micronuclei.
Genetic Variation:
Occurs through conjugation, where two cells align, fuse, and exchange micronuclei, leading to genetic diversity, separate from the asexually driven binary fission reproduction method.
Feeding Mechanisms:
Mixotrophic, heterotrophic, or autotrophic lifestyles can be adopted depending on the species.
Structure of Ciliates
Key components include:
Contractile vacuole
Cilia for movement
Oral groove and related structures for feeding processes.
Illustrative Features:
Contractile vacuole maintains osmotic balance.
Macro- and micronuclei have distinct functions in cellular genetics.
Conjugation Process in Paramecium
Fusion of Compatible Mates: Two mating-type cells align and partially fuse.
Meiosis of Micronuclei: Each cell undergoes meiosis, yielding haploid micronuclei.
Binary Fission Preparation: The cells proceed with binary fission, producing daughter cells.
Nuclear Exchange: The cells exchange a micronucleus.
Macronucleus Disintegration: The original macronucleus disintegrates, and a new structure forms from the exchanged micronucleus.
Final Separation: Cells separate post-conjugation, producing genetically diverse progeny.
Major Eukaryotic Lineages
Stramenopila (also known as Heterokonta)
Characteristics:
Possess flagella covered with hollow hairs
Flagella present at some stage of life cycle
Synapomorphy: unique derived traits for classification
Diversity:
Many unicellular forms
Some multicellular species
Classification of Major Lineages of Eukaryotes
Unikonta
Contains:
Amoebozoa
Lobose amoebae
Cellular slime molds
Plasmodial slime molds
Opisthokonta
Fungi
Choanoflagellates
Animals
Excavata
Includes:
Parabasalids
Diplomonads
Euglenids
Kinetoplastids
Plantae
Includes:
Glaucophyte algae
Red algae
Green algae
Land plants
Rhizaria
Includes:
Actinopods
Foraminiferans
Chlorarachniophytes
Alveolata
Includes:
Ciliates
Dinoflagellates
Apicomplexans
Stramenopila again highlighted:
Water molds
Diatoms
Brown algae
Diversity of Stramenopila
Important photosynthetic organisms:
Include diatoms, golden algae, brown algae, and water molds
Movement and Morphology:
Flagella with hollow projections
Diatoms and brown algae have chloroplasts
Diatoms form ornate glass-like shells
Reproduction:
Both asexual and sexual reproduction
Many exhibit diploid-dominant life cycles
Brown algae (e.g., kelp) undergo alternation of generations
Relevance:
Example of Phytophthora infestans causing the Irish potato famine
Diatoms are significant primary producers
Giant kelp forests provide habitats for diverse animals
Diatoms
Description:
Unicellular algae possessing a unique two-part glass-like wall made up of silica ()
Crucial for phytoplankton
Fossilized diatom walls compose diatomaceous earth
Golden Algae
Characteristics:
Named for color due to yellow and brown carotenoids
Cells usually biflagellated
Both flagella near one end
Photosynthetic and some mixotrophic
Predominantly unicellular but can form colonies
Mostly aquatic
Brown Algae
Features:
Largest and most complex algae
All species are multicellular
Mostly marine
Structures similar to plants:
Holdfast
Stipe
Blades
Giant seaweeds (kelps) can live in relatively deep ocean waters
Life Cycles of Brown Algae
Complexity:
Most brown algae exhibit alternation of generations
Alternation includes:
Multicellular haploid and diploid forms
Heteromorphic generations: structurally different
Isomorphic generations: visually similar
Life Cycle of Laminaria (Brown Alga)
Phases:
Haploid (n) and diploid (2n) stages
Diagram representation:
Sporangia
Meiosis leading to zoospores
Gametophytes (male and female)
Fertilization results in a zygote (2n) forming a mature female gametophyte leading to a developing sporophyte
Themes in Protist Diversity
Key Characteristics:
Extremely diverse in:
Size
Habitat
Morphology
Paraphyletic nature:
Lack of shared derived characteristics among different lineages
Eukaryotic Structure and Origin
Nuclear Structure
Eukaryotes contain a nucleus
Hypothesis on Nuclear Envelope Origin:
Derives from infoldings of the plasma membrane
Infoldings may have led to the development of the endoplasmic reticulum (ER) at the same time
Evidence: Infoldings of plasma membrane found in some bacteria; nuclear envelope is continuous with the ER in eukaryotes
Nuclear Envelope Functions
Separates transcription and translation
Diversification of nuclei led to unique forms in major protist lineages
Nuclear structure serves as a synapomorphy that distinguishes certain lineages and monophyletic groups
Endosymbiosis Theory
Mitochondria
Function:
Generate ATP
Theory:
Mitochondria originated when a bacterial cell established residence within another cell around 2 billion years ago
Concept of symbiosis where two different species live in physical contact; specifically endosymbiosis refers to one organism living inside another
Example of endosymbiosis and symbiotic prokaryotes remains common today
Supporting Evidence for Endosymbiosis
Characteristics consistent with endosymbiosis theory for mitochondria:
Size similar to α-proteobacteria
Replication by fission like bacteria
Own ribosomes and protein synthesis capability
Double membranes indicating engulfment
Possess their own genomes, organized in circular molecules similar to bacterial chromosomes
Phylogenetic Data:
Mitochondrial gene sequences show closer relation to α-proteobacteria than to eukaryotic nuclear DNA, indicating prokaryotic origin
Origin of Chloroplasts
Another instance of endosymbiosis:
Photosynthesis originated in protists through primary endosymbiosis
Cyanobacteria contain PSI and PSII
All photosynthetic protists possess chloroplasts
Hypothesis:
Eukaryotic chloroplasts originated when a protist engulfed a cyanobacterium
Supporting Evidence for Chloroplast Origin
Similar to mitochondria:
Chloroplasts display bacteria-like characteristics
Possess circular DNA with genes akin to cyanobacteria
Presence of peptidoglycan in cell walls
Existing endosymbiotic cyanobacteria found living within protist and animal cells
Hypothesis on Chloroplast Endosymbiosis
Biologists suggest primary endosymbiosis leading to photosynthesis first occurred in the common ancestor of the Plantae
This ancestor led to all Plantae subgroups
Chloroplasts also found in four other major protist lineages; in these cases, chloroplasts encased in multiple membranes
Secondary Endosymbiosis:
Ancestors of certain protists acquired their chloroplasts through secondary endosymbiosis
Photosynthesis Evolution in Protists
Photosynthesis arose in protists by primary endosymbiosis and spread to different lineages via secondary endosymbiosis
Biochemical connections exist between chloroplasts in alveolates and stramenopiles with red algae, and chloroplasts in euglenids and chlorarachniophytes with green algae
Notably, only dinoflagellates, diatoms, and brown algae exhibit photosynthetic species in the alveolates and stramenopiles, while the chloroplasts in ciliates, apicomplexans, and water molds have either been lost or functionally altered.