Protists: Classification, Diversity, and the Molecular Revolution

Evolutionary Classification and the Legacy of Microscopy

• The study of protests is utilized as a primary example of how the classification of organisms evolves, leading to the discovery of new broad-level and kingdom-level taxa.
• Protests were recognized relatively early due to the rise of microscopy, as these organisms are often significantly small in scale.
• Historical timeline of classification:
  • Mid-nineteenth century: Protests were separated from the plant and animal kingdoms. At this time, since the era of Linnaeus, plants included organisms now classified as fungi.
  • Protests functioned as a catch-all group for small organisms that did not fit the conceptual definitions of plants or animals as they were understood then.
  • Mid-1970s: The rise of domains occurred with the recognition of Archaea and Bacteria.
  • 1990s: Three distinct domains were established: Archaea, Bacteria, and Eukaryota.
  • Current Status: Protests are recognized as eukaryotes. Recently (as of February), they have been classified effectively into two kingdoms, though this area remains highly unsettled.
• The classification of prokaryotes, eukaryotes, protozoa, and Cremista is identified as the area where future taxonomic changes are most likely to occur.

The Genomic Revolution and the Burki et al. Study

• The molecular revolution has transformed the understanding of biological relationships, particularly for microorganisms.
• Small organisms possess fewer morphological characters (physical traits), making it difficult to categorize them based on appearance alone.
• Past classifications often grouped small organisms together based on similar characteristics that were co-evolved (convergent) due to environmental niches, rather than reflecting genuine evolutionary relationships.
• Burki et al. (2020) Trends in Ecology and Evolution:
  • This paper investigated the relationships between major groups of eukaryotes.
  • Eukaryotes are defined by membrane-lined compartments within cells, such as the cell nucleus and mitochondria, which distinguish them from prokaryotes (archaea and bacteria).
  • The study revealed that eukaryotic diversity is far more complex than a simple split into kingdoms like protozoa and Cremista.
  • While most named species belong to multicellular groups (Metazoa/animals, land plants, and fungi), these represent only a small fraction of higher-level eukaryotic diversity.
  • Dozens of new kingdom-level taxa have been identified within the group formerly known as protests.

Redefining Protests as a Term of Convenience

• Taxonomically, any eukaryote that is not a plant, fungus, or animal was traditionally classified as a protest, specifically within the kingdoms Cremista or Protozoa.
• The term "protest" is now considered a "term of convenience" rather than a natural group of related taxa (phylogenetic clade).
• Nesting of Kingdoms:
  • The major kingdoms of Fungi, Plantae, and Animalia are actually nested within the broader family tree of protests.
  • Gene sequencing and genome analysis allow researchers to identify relationships that morphology cannot reveal.
• Major Clades and Phylogenetic Structure:
  • Kingdom Plantae: Formed by the Glauquefyta, Chloroplastidae, and Rhodophytes (red algae). This is a distinct clade sharing a common ancestor.
  • Amorphia Clade: Includes the group Obazoa, which branches into Fungi and Animalia.
  • SAR: An acronym representing three major lineages (Stramenopiles, Alveolates, and Rhizaria).
  • Other clades include Heptista and Cryptista.
  • There are estimated to be between $8$ and $12$ kingdom-level groups currently identified within the eukaryotic tree.

Diversity in Form, Function, and Ecology

• Protests represent hundreds of thousands of species across various evolutionary branches.
• The SAR group alone contains approximately half of all described taxa in this category.
• Biological Structures:
  • Can be single-celled (unicellular), colonial, or a combination of both.
  • Can be multicellular, such as brown seaweeds.
• Energy Sources and Lifestyles:
  • Photosynthetic autotrophs: Such as various algae.
  • Parasitic: Living off host organisms.
  • Symbiotic: Living in partnership, such as those in the guts of termites and cockroaches that help break down cellulose for nutrient recycling.
  • Predatory heterotrophs: Engulfing particles and other organisms.
• Many protests are aquatic or cryptic, requiring specialized searches to locate.

Amoebozoa and the Ecology of Slime Molds

• Amoebozoa are typically single-celled organisms with a nucleus.
• Locomotion and Feeding:
  • They exhibit an amoeboid shape and develop pseudopods ("false feet").
  • These structures are used to move and capture prey, including bacteria and other single-celled protests.
• Slime Molds:
  • This is a term of convenience reflecting a lifestyle rather than a single phylogenetic group.
  • Most belong to Amoebozoa (part of the Amorphia group), though they were historically thought to be related to fungi.
  • Life Cycle: They spend most of their time as single cells moving through substrates. Under certain conditions, they aggregate into a mass of cells to create a fruiting body to produce reproductive spores.
  • Example: Fulgo (the "dog's vomit" slime mold), found globally.
• Ecological Interactions:
  • Certain invertebrates feed exclusively (obligate feeders) on slime molds.
  • Aspidiferous beetles (family Spindidae) are distributed worldwide and feed on the spores of slime molds like Fulgo.
  • Acanthonyura springtails are also thought to feed exclusively on slime mold fruiting bodies, such as those of the genus Trichia.

Diatoms and Brown Algae: Global Productivity

• Brown Algae:
  • Includes seaweeds like kelp.
  • Giant kelp (found in regions like California) creates underwater forests that are essential for ecosystem productivity.
  • Growth rate: Kelp can grow up to $0.5\,m$ every day.
• Diatoms:
  • Small, photosynthetic microalgae with bodies composed of silica ($SiO_2$).
  • Habitat: Marine environments, freshwater, soil, and moss.
  • Significant Oxygen Production: It is estimated that diatoms produce between $30\%$ and $50\%$ of the Earth's total oxygen.
  • They are planktonic (live in surface waters) and form "siliceous ooze" on the ocean floor when they die.
  • Environmental Indicators: Diatoms are used to reconstruct environmental history. Different taxa specialize in clean vs. dirty water, or high vs. low salinity. Core samples of lake or marine beds allow scientists to count species and determine past environmental conditions.

Plasmodium and the Impact of Malaria

• The genus Plasmodium consists of obligate parasitic protests, with several hundred known species.
• Life Cycle: Complex cycle involving both an insect stage (mostly mosquitoes) and a vertebrate/mammal stage.
• Global Health Impact:
  • The World Health Organization (WHO) estimated $620,000$ deaths globally in $2020$ due to malaria.
  • Distributions are largely restricted to warmer tropical regions where mosquito hosts can complete their life cycles.
• Environmental Case Study: Hawaii:
  • Before the arrival of Polynesians around $1200$ AD, there were no mosquitoes in Hawaii.
  • The absence of mosquitoes meant an absence of Plasmodium and malaria, resulting in native birds having no immunity.
  • Introduction of mosquitoes led to a collapse of the avian fauna (bird populations).
  • Altitude Refuge: Mosquitoes are range-restricted by temperature. Higher elevations (over $4,000\,m$ in Maui and the Big Island) remain too cool for the mosquitoes, protecting high-altitude bird species.
  • Climate Change Feedback: Increasing global temperatures allow mosquitoes to survive at higher elevations. This causes a loss of suitable protected habitat for endangered birds, as higher elevations often transition from forest to open habitats.

Common Names and the Persistence of Misclassification

• Euglenoids (Euglena):
  • Unicellular flagellates common in freshwater.
  • Historically classified as plants (because they photosynthesize) and animals (because they swim).
  • Now recognized as a distinct group of protests with a few thousand species.
• Water Molds (Phytophthora):
  • Phytophthora species are protests, not fungi, despite being commonly called "cinnamon fungus."
  • Historical Impact: Phytophthora had a catastrophic impact on potato crops in rural Ireland in the mid-nineteenth century.
  • This caused the Irish Potato Famine, leading to mass mortality and a massive diaspora of Irish people to the United States and Australia.
• Naming Issues: Common names often persist long after scientific classification has changed. Names like "algae," "slime mold," and "mold" frequently describe lifestyles or physical appearances rather than true phylogenetic relationships.