Marine protists

Marine protists are defined by their habitat as protists that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Life originated as marine single-celled prokaryotes (bacteria and archaea) and later evolved into more complex eukaryotes. Eukaryotes are the more developed life forms known as plants, animals, fungi and protists. Protists are the eukaryotes that cannot be classified as plants, fungi or animals. They are mostly single-celled and microscopic. The term protist came into use historically as a term of convenience for eukaryotes that cannot be strictly classified as plants, animals or fungi. They are not a part of modern cladistics because they are paraphyletic (lacking a common ancestor for all descendants).

Most protists are too small to be seen with the naked eye. They are highly diverse organisms currently organised into 18 phyla, but not easy to classify. Studies have shown high protist diversity exists in oceans, deep sea-vents and river sediments, suggesting large numbers of eukaryotic microbial communities have yet to be discovered. There has been little research on mixotrophic protists, but recent studies in marine environments found mixotrophic protists contribute a significant part of the protist biomass. Since protists are eukaryotes (and not prokaryotes) they possess within their cell at least one nucleus, as well as organelles such as mitochondria and Golgi bodies. Many protist species can switch between asexual reproduction and sexual reproduction involving meiosis and fertilization.

In contrast to the cells of prokaryotes, the cells of eukaryotes are highly organised. Plants, animals and fungi are usually multi-celled and are typically macroscopic. Most protists are single-celled and microscopic. But there are exceptions. Some single-celled marine protists are macroscopic. Some marine slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms. Other marine protist are neither single-celled nor microscopic, such as seaweed.

Protists have been described as a taxonomic grab bag of misfits where anything that does not fit into one of the main biological kingdoms can be placed. Some modern authors prefer to exclude multicellular organisms from the traditional definition of a protist, restricting protists to unicellular organisms. This more constrained definition excludes all brown, the multicellular red and green algae, and, sometimes, slime molds (slime molds excluded when multicellularity is defined as "complex").

Background
The ocean represents the largest continuous planetary ecosystem, hosting an enormous variety of organisms, which include microscopic biota such as unicellular eukaryotes (protists). Despite their small size, protists play key roles in marine biogeochemical cycles and harbour tremendous evolutionary diversity. Notwithstanding their significance for understanding the evolution of life on Earth and their role in marine food webs, as well as driving biogeochemical cycles to maintain habitability, little is known about their cell biology including reproduction, metabolism and signaling. Most of the biological knowledge available is based on comparison of proteins from cultured species to homologs in genetically tractable model taxa. A main impediment to understanding the cell biology of these diverse eukaryotes is that protocols for genetic modification are available for only a small number of species that represent neither the most ecologically relevant protists nor the breadth of eukaryotic diversity. Even so, in the decade to 2020, genome  and transcriptome sequencing initiatives have resulted in nearly 120 million unigenes being identified in protists, which is facilitating the development of genetic tools for model species.





Trophic modes
Protists can be divided broadly into four groups depending on whether their nutrition is plant-like, animal-like, fungal-like, or a mixture of these.

The fungus-like protist saprobes are specialized to absorb nutrients from nonliving organic matter, such as dead organisms or their wastes. For instance, many types of oomycetes grow on dead animals or algae. Marine saprobic protists have the essential function of returning inorganic nutrients to the water. This process allows for new algal growth, which in turn generates sustenance for other organisms along the food chain. Indeed, without saprobe species, such as protists, fungi, and bacteria, life would cease to exist as all organic carbon became "tied up" in dead organisms.

Mixotrophs
Mixotrophs have no single trophic mode. A mixotroph is an organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode on the continuum from complete autotrophy at one end to heterotrophy at the other. It is estimated that mixotrophs comprise more than half of all microscopic plankton. There are two types of eukaryotic mixotrophs: those with their own chloroplasts, and those with endosymbionts—and others that acquire them through kleptoplasty or by enslaving the entire phototrophic cell.

The distinction between plants and animals often breaks down in very small organisms. Possible combinations are photo- and chemotrophy, litho- and organotrophy, auto- and heterotrophy or other combinations of these. Mixotrophs can be either eukaryotic or prokaryotic. They can take advantage of different environmental conditions.

Recent studies of marine microzooplankton found 30–45% of the ciliate abundance was mixotrophic, and up to 65% of the amoeboid, foram and radiolarian biomass was mixotrophic.

Phaeocystis is an important algal genus found as part of the marine phytoplankton around the world. It has a polymorphic life cycle, ranging from free-living cells to large colonies. It has the ability to form floating colonies, where hundreds of cells are embedded in a gel matrix, which can increase massively in size during blooms. As a result, Phaeocystis is an important contributor to the marine carbon and sulfur cycles. Phaeocystis species are endosymbionts to acantharian radiolarians.

Protist locomotion
Another way of categorising protists is according to their mode of locomotion. Many unicellular protists, particularly protozoans, are motile and can generate movement using flagella, cilia or pseudopods. Cells which use flagella for movement are usually referred to as flagellates, cells which use cilia are usually referred to as ciliates, and cells which use pseudopods are usually referred to as amoeba or amoeboids. Other protists are not motile, and consequently have no movement mechanism.



Flagella are used in prokaryotes (archaea and bacteria) as well as protists. In addition, both flagella and cilia are widely used in eukaryotic cells (plant and animal) apart from protists.

The regular beat patterns of eukaryotic cilia and flagella generates motion on a cellular level. Examples range from the propulsion of single cells such as the swimming of spermatozoa to the transport of fluid along a stationary layer of cells such as in a respiratory tract. Though eukaryotic flagella and motile cilia are ultrastructurally identical, the beating pattern of the two organelles can be different. In the case of flagella, the motion is often planar and wave-like, whereas the motile cilia often perform a more complicated three-dimensional motion with a power and recovery stroke.

Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back and forth. Eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia.





Ciliates generally have hundreds to thousands of cilia that are densely packed together in arrays. Like the flagella, the cilia are powered by specialised molecular motors. An efficient forward stroke is made with a stiffened flagellum, followed by an inefficient backward stroke made with a relaxed flagellum. During movement, an individual cilium deforms as it uses the high-friction power strokes and the low-friction recovery strokes. Since there are multiple cilia packed together on an individual organism, they display collective behaviour in a metachronal rhythm. This means the deformation of one cilium is in phase with the deformation of its neighbor, causing deformation waves that propagate along the surface of the organism. These propagating waves of cilia are what allow the organism to use the cilia in a coordinated manner to move. A typical example of a ciliated microorganism is the Paramecium, a one-celled, ciliated protozoan covered by thousands of cilia. The cilia beating together allow the Paramecium to propel through the water at speeds of 500 micrometers per second.

Marine algae
Algae is an informal term for a widespread and diverse group of photosynthetic protists which are not necessarily closely related and are thus polyphyletic. Marine algae can be divided into six groups: green, red and brown algae, euglenophytes, dinoflagellates and diatoms.

Dinoflagellates and diatoms are important components of marine algae and have their own sections below. Euglenophytes are a phylum of unicellular flagellates with only a few marine members.

Not all algae are microscopic. Green, red and brown algae all have multicellular macroscopic forms that make up the familiar seaweeds. Green algae, an informal group, contains about 8,000 recognised species. Many species live most of their lives as single cells or are filamentous, while others form colonies made up from long chains of cells, or are highly differentiated macroscopic seaweeds. Red algae, a (disputed) phylum contains about 7,000 recognised species, mostly multicellular and including many notable seaweeds. Brown algae form a class containing about 2,000 recognised species, mostly multicellular and including many seaweeds such as kelp. Unlike higher plants, algae lack roots, stems, or leaves. They can be classified by size as microalgae or macroalgae.

Microalgae are the microscopic types of algae, not visible to the naked eye. They are mostly unicellular species which exist as individuals or in chains or groups, though some are multicellular. Microalgae are important components of the marine protists discussed above, as well as the phytoplankton discussed below. They are very diverse. It has been estimated there are 200,000–800,000 species of which about 50,000 species have been described. Depending on the species, their sizes range from a few micrometers (μm) to a few hundred micrometers. They are specially adapted to an environment dominated by viscous forces.

Macroalgae are the larger, multicellular and more visible types of algae, commonly called seaweeds. Seaweeds usually grow in shallow coastal waters where they are anchored to the seafloor by a holdfast. Like microalgae, macroalgae (seaweeds) can be regarded as marine protists since they are not true plants. But they are not microorganisms, so they are not within the scope of this article.

Unicellular organisms are usually microscopic, less than one tenth of a millimeter long. There are exceptions. Mermaid's wineglass, a genus of subtropical green algae, is single-celled but remarkably large and complex in form with a single large nucleus, making it a model organism for studying cell biology. Another single-celled algae, Caulerpa taxifolia, has the appearance of a vascular plant including "leaves" arranged neatly up stalks like a fern. Selective breeding in aquariums to produce hardier strains resulted in an accidental release into the Mediterranean where it has become an invasive species known colloquially as killer algae.

Diatoms


Diatoms are photosynthetic unicellular algae populating the oceans and other waters around the globe. They form a (disputed) phylum containing about 100,000 recognised species. Diatoms generate about 20 per cent of all oxygen produced on the planet each year, and take in over 6.7 billion metric tons of silicon each year from the waters in which they live. They produce 25–45% of the total primary production of organic material in the oceans, owing to their prevalence in open-ocean regions when total phytoplankton biomass is maximal.

Diatoms are enclosed in protective silica (glass) shells called frustules. They are classified by the shape of these glass cages in which they live, and which they build as they grow. Each frustule is made from two interlocking parts covered with tiny holes through which the diatom exchanges nutrients and wastes. Dead diatoms drift to the ocean floor where, over millions of years, the remains of their frustules can build up as much as half a mile deep. Diatoms have relatively high sinking speeds compared with other phytoplankton groups, and they account for about 40% of particulate carbon exported to ocean depths.

Coccolithophores
Coccolithophores are minute unicellular photosynthetic protists with two flagella for locomotion. Most of them are protected by calcium carbonate shells covered with ornate circular plates or scales called coccoliths. The term coccolithophore derives from the Greek for a seed carrying stone, referring to their small size and the coccolith stones they carry. Under the right conditions they bloom, like other phytoplankton, and can turn the ocean milky white.



Dinoflagellates
Dinoflagellates are usually positioned as part of the algae group, and form a phylum of unicellular flagellates with about 2,000 marine species. The name comes from the Greek "dinos" meaning whirling and the Latin "flagellum" meaning a whip or lash. This refers to the two whip-like attachments (flagella) used for forward movement. Most dinoflagellates are protected with red-brown, cellulose armour. Like other phytoplankton, dinoflagellates are r-strategists which under right conditions can bloom and create red tides. Excavates may be the most basal flagellate lineage.

By trophic orientation dinoflagellates are all over the place. Some dinoflagellates are known to be photosynthetic, but a large fraction of these are in fact mixotrophic, combining photosynthesis with ingestion of prey (phagotrophy). Some species are endosymbionts of marine animals and other protists, and play an important part in the biology of coral reefs. Others predate other protozoa, and a few forms are parasitic. Many dinoflagellates are mixotrophic and could also be classified as phytoplankton.

The toxic dinoflagellate Dinophysis acuta acquire chloroplasts from its prey. "It cannot catch the cryptophytes by itself, and instead relies on ingesting ciliates such as the red Mesodinium rubrum, which sequester their chloroplasts from a specific cryptophyte clade (Geminigera/Plagioselmis/Teleaulax)".

Marine protozoans
Protozoans are protists which feed on organic matter such as other microorganisms or organic tissues and debris. Historically, the protozoa were regarded as "one-celled animals", because they often possess animal-like behaviours, such as motility and predation, and lack a cell wall, as found in plants and many algae. Although the traditional practice of grouping protozoa with animals is no longer considered valid, the term continues to be used in a loose way to identify single-celled organisms that can move independently and feed by heterotrophy.

Marine protozoans include zooflagellates, foraminiferans, radiolarians and some dinoflagellates.

Radiolarians
Radiolarians are unicellular predatory protists encased in elaborate globular shells, typically between 0.1 and 0.2 millimetres in size, usually made of silica and pierced with holes. Their name comes from the Latin for "radius". They catch prey by extending parts of their body through the holes. As with the silica frustules of diatoms, radiolarian shells can sink to the ocean floor when radiolarians die and become preserved as part of the ocean sediment. These remains, as microfossils, provide valuable information about past oceanic conditions.

Foraminiferans
Like radiolarians, foraminiferans (forams for short) are single-celled predatory protists, also protected with shells that have holes in them. Their name comes from the Latin for "hole bearers". Their shells, often called tests, are chambered (forams add more chambers as they grow). The shells are usually made of calcite, but are sometimes made of agglutinated sediment particles or chiton, and (rarely) of silica. Most forams are benthic, but about 40 species are planktic. They are widely researched with well established fossil records which allow scientists to infer a lot about past environments and climates.

A number of forams are mixotrophic (see below). These have unicellular algae as endosymbionts, from diverse lineages such as the green algae, red algae, golden algae, diatoms, and dinoflagellates. Mixotrophic foraminifers are particularly common in nutrient-poor oceanic waters. Some forams are kleptoplastic, retaining chloroplasts from ingested algae to conduct photosynthesis.

Ciliates
Marine ciliates are major grazers of the phytoplankton.

Phytoplankton primary production supports higher trophic levels and fuels microbial remineralization. The dominant pelagic grazers of phytoplankton are typically associated with distinct operating modes of the food web compartments and nutrient cycling. Heterotrophic protist grazers and microzooplankton dominance is usually associated with the microbial loop and regenerated production; while mesozooplankton is associated with a linear food chain and export production. Grazing on particulate primary production in the global ocean surface is ~10–15% for mesozooplankton and 59–75% for microzooplankton,  with estimates for coastal and estuarine systems usually in the a lower range.

Ciliates constitute an important component of the microzooplankton community with preference for small-sized preys, in contrast to mesozooplankton, and many ciliate species are also grazed by mesozooplankton. Thus, ciliates can be an important link between small cells and higher trophic levels. Besides their significant role in carbon transfer, ciliates are also considered high quality food, as a source of proteinaceous compounds with a low C:N ratio in comparison to phytoplankton.



Although many ciliates are heterotrophs, a number of pelagic species are mixotrophic, combining both phagotrophic and phototrophic nutrition (Stoecker, 1998). The recognition of mixotrophy in the marine plankton food web has challenged the classical understanding of pelagic food webs, as autotrophy and heterotrophy are not necessarily two distinct functional compartments. Classical understanding of ecological interactions among plankton, such as competition for nutrients, indicates that nutrient uptake affinity decreases with organism size, favoring smaller sizes under resource limiting conditions. Mixotrophy is advantageous to organisms under nutrient limited conditions, allowing them to reduce direct competition by grazing on smaller prey and increase direct ingestion of nutrients. Modeling results suggest that mixotrophy favors larger organisms, and therefore enhances trophic transfer efficiency. On top of that, mixotrophy appears to be important over both, space and time, in marine systems. stressing the need for ecological field studies to further elucidate the role of mixotrophy.

Interactome




Interaction between microbial species has played important roles in evolution and speciation. One of the best examples is that the origin of eukaryotes is grounded in the interaction-events of endosymbiosis; giving rise to mitochondria, chloroplasts, and other metabolic capacities in the eukaryotic cell,   Microbial interactions guarantee ecosystem function, having crucial roles in, for instance, carbon channeling in photosymbiosis, control of microalgae blooms by parasites, and phytoplankton-associated bacteria influencing the growth and health of their host.

Despite their importance, understanding of microbial interactions in the ocean and other aquatic systems is rudimentary, and the majority of them are still unknown. The earliest surveys of interactions between aquatic microbes date back to the 19th century. In 1851, while on board HMS Rattlesnake in the Pacific Ocean, Thomas Huxley discovered small yellow–green cells inside the conspicuous planktonic radiolarians which he thought were organelles. Later, Karl Brandt established the yellowish cells were symbiotic alga and named them zooxanthella. Since these early studies, hundreds of others have reported microbial interactions by using classic tools, mainly microscopy, but this knowledge has not yet been gathered into one accessible database. In recent years the high throughput sequencing (HTS)  of environmental DNA or RNA has transformed understanding of microbial diversity and evolution, as well as generating hypotheses on microbial interactions based on correlations of estimated microbial abundances over spatiotemporal scales.

The diagram on the right is an overview of the interactions between planktonic protists recorded in a manually curated Protist Interaction DAtabase (PIDA). The network is based on 2422 ecological interactions in the PIDA registered from ~500 publications spanning the last 150 years. The nomenclature and taxonomic order of Eukaryota is based on Adl et al. 2019. The nomenclature and taxonomic order of Bacteria is based on Schultz et al. 2017.

The nodes are grouped (outer circle) according to eukaryotic supergroups (or Incertae sedis), Bacteria and Archaea. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39%), followed by symbiosis (29%), parasitism (18%), and unresolved interactions (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Nodes represent eukaryotic and prokaryotic taxa and are colored accordingly. Node size indicates the number of edges/links that are connected to that node. Each node/taxon is assigned a number, which corresponds with the numbers for taxa in B, C and D. Edges represent interactions between two taxa and are colored according to ecological interaction type: predation (orange), symbiosis (green), and parasitism (purple).

The network is undirected, meaning that a node can contain both parasites/symbionts/prey and hosts/predators. To avoid cluttering of the figure, "Self-loops", which represent cases where both interacting organisms belong to the same taxon (e.g., a dinoflagellate eating another dinoflagellate) are not shown as edges/links in this figure, but are considered in the size of nodes. The outermost circle groups taxa in the different eukaryotic ‘supergroups’ or the prokaryotic domains Bacteria and Archaea. Ancryomonadidae is abbreviated An. Telonema is not placed into any of the supergroups, but classified as Incertae sedis (abbreviated I.S. in the figure). In B, B, and D the following abbreviations for supergroups are used: Ar Archaea, Ba Bacteria, Rh Rhizaria, Al Alveolata, St Stramenopiles, Ha Haptista, Cy Cryptista, Ap Archaeplastida, Ex Excavata, Ob Obazoa, Am Amoebozoa, Cu CRuMS, An Ancryomonadidae, Is Incertae sedis.

B: Predator–prey interactions in PIDA. The node numbers correspond to taxa node numbers in a. Abbreviations for supergroups are described above. Background and nodes are colored according to functional role in the interaction: Prey are colored light orange (left part of figure), while predators are depicted in dark orange (right part of figure). The size of each node represents the number of edges connected to that node.

C. Symbiont–host interactions included in PIDA. The node numbers correspond to node numbers in A. Abbreviations for supergroups are described above. Symbionts are to the left, colored light green, and their hosts are to the right in dark green. The size of each node represents the number of edges connected to that node.

D: Parasite–host interactions included in PIDA. The node numbers correspond to node numbers in A. Abbreviations for supergroups are described above. Parasite taxa are depicted in light purple (left), hosts in dark purple (right).

It was found that protist predators seem to be "multivorous" while parasite–host and symbiont–host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (Tara expedition) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions.

Protist shells
Many protists have protective shells or tests, usually made from calcium carbonate (chalk) or silica (glass). Protists are mostly single-celled and microscopic. Their shells are often tough mineralised forms that resist degradation, and can survive the death of the protist as a microfossil. Although protists are very small, they are ubiquitous. Their numbers are such that their shells play a huge part in the formation of ocean sediments, and in the global cycling of elements and nutrients.

Diatom shells are called frustules and are made from silica. These glass structures have accumulated for over 100 million years leaving rich deposits of nano and microstructured silicon oxide in the form of diatomaceous earth around the globe. The evolutionary causes for the generation of nano and microstructured silica by photosynthetic algae are not yet clear. However, in 2018 it was shown that reflection of ultraviolet light by nanostructured silica protects the DNA in the algal cells, and this may be an evolutionary cause for the formation of the glass cages. Coccolithophores are protected by a shell constructed from ornate circular plates or scales called coccoliths. The coccoliths are made from calcium carbonate or chalk. The term coccolithophore derives from the Greek for a seed carrying stone, referring to their small size and the coccolith stones they carry.

There are benefits for protists that carry protective shells. The diagram on the left above shows some benefits coccolithophore get from carrying coccoliths. In the diagram, (A) represents accelerated photosynthesis including carbon concentrating mechanisms (CCM) and enhanced light uptake via scattering of scarce photons for deep-dwelling species. (B) represents protection from photodamage including sunshade protection from ultraviolet light (UV) and photosynthetic active radiation (PAR) and energy dissipation under high-light conditions. (C) represents armour protection includes protection against viral/bacterial infections and grazing by selective and nonselective grazers.

There are also costs for protists that carry protective shells. The diagram on the right above shows some of the energetic costs coccolithophore incur from carrying coccoliths. In the diagram, the energetic costs are reported in percentage of total photosynthetic budget. (A) represents transport processes include the transport into the cell from the surrounding seawater of primary calcification substrates Ca2+ and HCO3− (black arrows) and the removal of the end product H+ from the cell (gray arrow). The transport of Ca2+ through the cytoplasm to the coccolith vesicle (CV) is the dominant cost associated with calcification. (B) represents metabolic processes include the synthesis of coccolith-associated polysaccharides (CAPs – gray rectangles) by the Golgi complex (white rectangles) that regulate the nucleation and geometry of CaCO3 crystals. The completed coccolith (gray plate) is a complex structure of intricately arranged CAPs and CaCO3 crystals. (C) Mechanical and structural processes account for the secretion of the completed coccoliths that are transported from their original position adjacent to the nucleus to the cell periphery, where they are transferred to the surface of the cell.

Further references

 * CC-BY icon.svg Available under a Creative Commons Attribution 4.0 International License.