Protist


A protist or protoctist is any eukaryotic organism that is not an animal, land plant, or fungus. Protists do not form a natural group, or clade, but are a paraphyletic grouping of all descendants of the last eukaryotic common ancestor excluding land plants, animals, and fungi.
Protists were historically regarded as a separate taxonomic kingdom known as Protista or Protoctista. With the advent of phylogenetic analysis and electron microscopy studies, the use of Protista as a formal taxon was gradually abandoned. In modern classifications, protists are spread across several eukaryotic clades called supergroups, such as Archaeplastida, SAR, Obazoa, Amoebozoa and "Excavata".
Protists represent an extremely large genetic and ecological diversity in all environments, including extreme habitats. Their diversity, larger than for all other eukaryotes, has only been discovered in recent decades through the study of environmental DNA and is still in the process of being fully described. They are present in all ecosystems as important components of the biogeochemical cycles and trophic webs. They exist abundantly and ubiquitously in a variety of mostly unicellular forms that evolved multiple times independently, such as free-living algae, amoebae and slime moulds, or as important parasites. Together, they compose an amount of biomass that doubles that of animals. They exhibit varied types of nutrition, sometimes combining them. They present unique adaptations not present in multicellular animals, fungi or land plants. The study of protists is termed protistology.

Definition

Protists are a diverse group of eukaryotes that are primarily single-celled and microscopic and exhibit a wide variety of shapes and life strategies. They have different life cycles, trophic levels, modes of locomotion, and cellular structures. Although most protists are unicellular, there is a considerable range of multicellularity amongst them; some form colonies or multicellular structures visible to the naked eye. The term 'protist' refers to all eukaryotes that are not animals, land plants or fungi, the three traditional eukaryotic kingdoms. Because of this definition by exclusion, protists compose a paraphyletic group that includes the ancestors of those three kingdoms.
The names of some protists, because of their mixture of traits similar to both animals and land plants or fungi, have been published under either or both of the botanical and the zoological codes of nomenclature.

Common types

Protists display a wide range of distinct morphological types that have been used to classify them for practical purposes, although most of these categories do not represent evolutionary cohesive lineages or clades and have instead evolved independently several times. The most recognizable types are:
  • Amoebae. Characterized by their irregular, flexible shapes, these protists move by extending portions of their cytoplasm, known as pseudopodia, to crawl along surfaces. Many groups of amoebae are naked, but testate amoebae and foraminifera grow a shell around their cell made from digested material or surrounding debris. Some, known as radiolarians and heliozoans, have special spherical shapes with microtubule-supported pseudopodia radiating from the cell. Some amoebae are capable of producing stalked multicellular stages that bear spores, often by aggregating together; these are known as slime molds. The main clades containing amoebae are Amoebozoa and Rhizaria. Even some individual amoebae can grow to giant sizes visible to the naked eye.
  • Flagellates. These protists are equipped with one or more whip-like appendages called cilia, undulipodia or eukaryotic flagella, which enable them to swim or glide freely through the environment. Flagellates are found in all lineages, reflecting that the common ancestor of all living eukaryotes was a flagellate. They usually exhibit two cilia, but there are a number of flagellate groups with a high number of cilia. Some groups, such as the well-known ciliates and the parasitic opalinids, have a cell surface covered in rows of cilia that beat rhythmically. A few groups of amoebae have retained their flagella, making them amoeboflagellates.
  • Algae. They are the photosynthetic protists, and can be found in most of the main clades, completely intermingled with heterotrophic protists which are traditionally called protozoa. Algae exhibit the most diverse range of morphologies, from single flagellated or coccoid cells to amoeboid cells to colonial and multicellular macroscopic forms.
  • Fungus-like protists. Several clades of protists have evolved an appearance similar to fungi through hyphae-like structures and a saprophytic nutrition. They have evolved multiple times, often very distantly from true fungi.
  • Sporozoa. This category traditionally included parasitic protists that reproduced via spores. Its current use is restricted to the apicomplexans, such as Plasmodium falciparum, the cause of malaria.

    Diversity

The species diversity of protists is severely underestimated by traditional methods that differentiate species based on morphological characteristics. The number of described protist species is very low in comparison to the diversity of land plants, animals and fungi, which are historically and biologically well-known and studied. The predicted number of species also varies greatly, ranging from 140,000 to 1,600,000, and in several groups the number of predicted species is arbitrarily doubled. Most of these predictions are highly subjective. Molecular techniques such as environmental DNA barcoding have revealed a vast diversity of undescribed protists that accounts for the majority of eukaryotic sequences or operational taxonomic units, dwarfing those from land plants, animals and fungi. As such, it is considered that protists dominate eukaryotic diversity.
The evolutionary relationships of protists have been explained through molecular phylogenetics, the sequencing of entire genomes and transcriptomes, and electron microscopy studies of the flagellar apparatus and cytoskeleton. New major evolutionary lineages of protists and novel biodiversity continue to be discovered, resulting in dramatic changes to the eukaryotic tree of life. Protists are currently divided into various large clades informally named supergroups. Most photosynthetic eukaryotes fall under the Diaphoretickes clade, which contains the supergroups Archaeplastida and SAR, as well as the phyla Telonemia, Cryptista and Haptista. The animals and fungi fall into the Amorphea supergroup, which contains the phylum Amoebozoa and several other protist lineages. Various groups of eukaryotes with primitive cell architecture are collectively known as the "Excavata".

"Excavata"

"Excavata" is a group that encompasses diverse protists, mostly flagellates, ranging from aerobic and anaerobic predators to phototrophs and heterotrophs. The common name 'excavate' refers to the common characteristic of a ventral groove in the cell used for suspension feeding, which is considered to be an ancestral trait present in the last eukaryotic common ancestor. The "Excavata" is composed of three clades: Discoba, Metamonada and Malawimonadida, each including 'typical excavates' that are free-living phagotrophic flagellates with the characteristic ventral groove. According to most phylogenetic analyses, this group is paraphyletic, with some analyses placing the root of the eukaryote tree within Metamonada.
Discoba includes three major groups: Jakobida, Euglenozoa and Heterolobosea. Jakobida are a small group of free-living heterotrophic flagellates, with two cilia, that primarily eat bacteria through suspension feeding; most are aquatic aerobes, with some anaerobic species, found in marine, brackish or fresh water. They are best known for their bacterial-like mitochondrial genomes. Euglenozoa is a rich group of flagellates with very different lifestyles, including: the free-living heterotrophic and photosynthetic euglenids ; the free-living and parasitic kinetoplastids ; the deep-sea anaerobic symbiontids; and the elusive diplonemids. Heterolobosea are a collection of amoebae, flagellates and amoeboflagellates with complex life cycles, among which are some slime molds. The two clades Euglenozoa and Heterolobosea are sister taxa, united under the name Discicristata, in reference to their mitochondrial cristae shaped like discs. The species Tsukubamonas globosa is a free-living flagellate whose precise position within Discoba is not yet settled, but is probably more closely related to Discicristata than to Jakobida.
The metamonads are a phylum of completely anaerobic or microaerophilic protozoa, primarily flagellates. Some are gut symbionts of animals such as termites, others are free-living, and others are parasitic. They include three main clades: Fornicata, Parabasalia and Preaxostyla. Fornicata encompasses the diplomonads, with two nuclei, and several smaller groups of free-living, commensal and parasitic protists. Parabasalia is a varied group of anaerobic, mostly endobiotic organisms, ranging from small parasites to giant intestinal symbionts with numerous flagella and nuclei found in wood-eating termites and cockroaches. Preaxostyla includes the anaerobic and endobiotic oxymonads, with modified mitochondria, and two genera of free-living microaerophilic bacterivorous flagellates Trimastix and Paratrimastix, with typical excavate morphology. Two genera of anaerobic flagellates of recent description and unique cell architecture, Barthelona and Skoliomonas, are closely related to the Fornicata.
The malawimonads are a small group of freshwater or marine suspension-feeding bacterivorous flagellates with typical excavate appearance, closely resembling Jakobida and some metamonads but not phylogenetically close to either in most analyses.