Ochrophyte

Ochrophytes, also known as heterokontophytes or stramenochromes, are a group of algae. They are the photosynthetic stramenopiles, a group of eukaryotes, organisms with a cell nucleus, characterized by the presence of two unequal flagella, one of which has tripartite hairs called mastigonemes. In particular, they are characterized by photosynthetic organelles or plastids enclosed by four membranes, with membrane-bound compartments called thylakoids organized in piles of three, chlorophyll a and c as their photosynthetic pigments, and additional pigments such as β-carotene and xanthophylls. Ochrophytes are one of the most diverse lineages of eukaryotes, containing ecologically important algae such as brown algae and diatoms. They are classified either as phylum Ochrophyta or Heterokontophyta, or as subphylum Ochrophytina within phylum Gyrista. Their plastids are of red algal origin.

Description
Ochrophytes are eukaryotic organisms composed of cells that are either naked or covered by scales, lorica or a cell wall. They can be single-celled, colonial, coenocytic or multicellular. Some Phaeophyceae develop as large multicellular thalli with differentiated tissues. All ochrophytes uniformly have tubular mitochondrial cristae. This is a common trait shared with their relatives, heterotrophic stramenopiles, as well as other closely related groups such as Rhizaria, Telonemia and Alveolata. As primarily photosynthetic eukaryotes, they are considered algae, distinguished from other groups of algae by specific morphological and ultrastructural traits, such as their flagella, chloroplasts and pigments.

Flagella
As stramenopiles (=heterokonts), their swimming cells frequently display two markedly unequal flagella: an anterior flagellum ("tinsel") with straw-like hollow tripartite hairs called mastigonemes, and an immature posterior smooth flagellum ("whiplash") lacking these hairs. The ciliary transition zone of the flagellum generally has a transitional helix.

Chloroplasts
The ochrophytes are mostly photosynthetic. As such, they may possess one or more photosynthetic plastids (chloroplasts) per cell. Some groups contain species with leucoplasts, chloroplasts that have lost photosynthetic capacity and pigments but presumably continue to play a role in the synthesis of aminoacids, lipids and heme groups. Ochrophytes have a distinct plastid ultrastructure in comparison to other algal groups. Their chloroplasts originate from an event of secondary endosymbiosis from a red alga, which lead to four surrounding membranes: two inner membranes, corresponding to the primary plastid membranes; a third membrane, corresponding to the plasma membrane of the red alga; and an outermost layer, corresponding to the phagosome membrane. This characteristic differentiates them from archaeplastid algae (glaucophytes, red algae and green algae), whose chloroplasts have only two membranes. The two outer layers of ochrophyte plastids are continguous with the endoplasmic reticulum (ER), together composing the chloroplast endoplasmic reticulum (CER), also known as the periplastidial endoplasmic reticulum (PER), which is often connected to the nuclear envelope. The tripartite flagellar hairs, characteristic of stramenopiles, are produced within either the PER or the nuclear envelope.

The periplastid compartment (PC), between the second and third layers, is a separate region that in other algal groups (i.e. cryptomonads and chlorarachniophytes) contains a nucleomorph, the vestigial nucleus of the secondary endosymbiont; however, no nucleomorphs are known within the ochrophytes. Instead, other structures have been observed within the PC, similarly to those seen in haptophytes and chromerid algae: "blob-like structures" where PC proteins are localized, and a vesicular network. Within the CER, there is a prominent region of tight direct contacts between the periplastid membrane and the inner nuclear envelope, where lipid transfers might occur, and perhaps exchange of other molecules.

Commonly, within the plastid stroma, three stacked thylakoids differentiate into the "girdle lamella", which runs around the periphery of the plastid, beneath the innermost membrane. The remaining thylakoids are arranged in stacks of three. In synchromophytes and aurearenophytes, a consortium of several plastids, each surrounded by two or three inner membranes respectively, is enveloped by a shared outer membrane.

Pigmentation
Ochrophyte chloroplasts contain chlorophylls a and c as photosynthetic pigments, in addition to fucoxanthin. Chlorophyll a binds to thylakoids, while the c pigment is present in the stroma. The most frequent accessory pigment in ochrophytes is the yellow β-carotene. The golden-brown or brown pigmentation in diatoms, brown algae, golden algae and others is conferred by the xanthophyll fucoxanthin. In the yellow-green or yellow-brown raphidophyceans, eustigmatophyceans and xanthophyceans, vaucheriaxanthin is dominant instead. These pigment combinations extend their photosynthetic ability beyond chlorophyll a alone. Additionally, xanthophylls protect the photosystems from high intensity light.

Storage products
Ochrophyte algae accumulate chrysolaminarin, a carbohydrate consisting of short chains of β-1,3-linked glucose molecules, as a storage product. It is stored in vesicles located within the cytoplasm, outside plastids, unlike other algae. Cytoplasmic lipid droplets are also common. They lack starch, which is the common storage product in green algae and plants.

Reproduction
Ochrophytes are capable of asexual reproduction by fragmentation, propagules, vegetative cell division, sporogenesis or zoosporogenesis. In addition, they are capable of sexual reproduction through gametes, by three different modes: isogamy, anisogamy or oogamy.

Ecology
Ochrophytes are present in nearly all environments. Some classes are more common in marine habitats, while others are more frequent in freshwater or soil. Among the ochrophyte lineages are the diatoms, the most abundant photosynthetic eukaryotes worldwide in marine habitats; multicellular seaweeds, such as brown algae (e.g., kelp) and golden algae; and an array of microscopic single-celled lineages that are also abundant, as evidenced by environmental sequencing. Regarding nutrition, various ochrophytes are mixotrophic, usually through phagocytosis.

Marine
Several classes of heterokont algae are exclusively known from marine habitats, such as Bolidophyceae, Pelagophyceae, Pinguiophyceae and Schizocladiophyceae. The brown algae (Phaeophyceae) are almost exclusively marine, with very few freshwater genera.

Freshwater
Chrysophyceae, Phaeothamniophyceae and Xanthophyceae are predominantly freshwater classes. In lotic habitats (rivers, streams), golden algae (Chrysophyceae) and yellow-green algae (Xanthophyceae) are common and occasionally abundant. The golden algal genus Hydrurus, in particular, can be widespread in some drainage basins and is common in cold, clear, fast-flowing mountain streams, where it attaches to a firm substrate. Xanthophycean genera commonly found in rivers include Vaucheria, Tribonema and Bumilleria, either freely floating or attached to filamentous algae and plants. Diatoms are more diverse, with more than 60 genera commonly found in rivers. Many river diatoms have developed different strategies to attach to the substrate to avoid being displaced by water currents. The most basic strategy is to produce extracellular polymeric substances, varied carbohydrate structures formed from the cell membrane. In faster-flowing waters, some diatoms (e.g., Cocconeis) grow directly attached to the substrate through adhesive films. Others (e.g., Eunotia, Nitzschia) grow stalks or colonial tubes capable of reaching higher into the water column to acquire more nutrients. Brown algae (Phaeophyceae), although highly diversified, contain only seven species present in rivers. These lack any complex multicellular thalli, and instead exist as benthic filamentous forms that have evolved independently from marine ancestors.

Harmful algae
Two main lineages of photosynthetic stramenopiles include many toxic species. Within the class Raphidophyceae, strains of Heterosigma and Chattonella at high concentrations are responsible for fish mortality, although the nature and action of their toxins is not resolved. Freshwater Gonyostomum species are capable of mucilage secretion at high amounts detrimental to fish gills. Within the diatoms (Bacillariophyta), harmful effects can be due to physical damage or to toxin production. Centric diatoms like Chaetoceros live as colonial chains of cells with long spines (setae) that can clog fish gills, causing their death. Among diatoms, the only toxin producers have been found among pennate diatoms, almost entirely within the genus Pseudonitzschia. More than a dozen species of Pseudonitzschia are capable of producing a neurotoxin, domoic acid, the cause of amnesiac shellfish poisoning.

External
The ochrophytes constitute a highly diverse clade within Stramenopila, a eukaryotic supergroup that also includes several heterotrophic lineages of protists such as oomycetes, hyphochytrids, labyrinthuleans, opalines and bicosoecids. This lineage of stramenopiles originated from an event of secondary endosymbiosis where a red alga was transformed into the chloroplast of the common ancestor of ochrophytes.

The total group of ochrophytes is estimated to have evolved between 874 and 543 million years ago (Ma) through molecular clock inference. However, the earliest fossil remains, assigned to the billion-year-old xanthophyte Palaeovaucheria, suggest that ochrophytes had appeared by 1000 Ma. Other early putative representatives of photosynthetic stramenopiles are Jacutianema (750 Ma), Germinosphaera (750–700 Ma) and the brown alga Miaohephyton (600–550 Ma). Scales similar to modern chrysophyte scales, and valves resembling the modern centric diatom valves, have been found in 800–700 million-years-old sediments.

Internal
Relationships among many classes of ochrophytes remain unresolved, but three main clades (called SI, SII and SIII) are supported in most phylogenetic analyses. The SI lineage, containing the diverse and multicellular class Phaeophyceae, or brown algae, experienced an evolutionary radiation during the late Paleozoic (around 310 million years ago). The class Schizocladiophyceae is the sister lineage to brown algae, followed by a clade of closely related classes Xanthophyceae, Phaeosacciophyceae and Chrysoparadoxophyceae. This is in turn the sister lineage to a clade containing Aurearenophyceae and Phaeothamniophyceae, which are sometimes treated as one class Aurophyceae. The Raphidophyceae are the most basal within the SI. The SII lineage contains the golden algae or Chrysophyceae, as well as smaller classes Synurophyceae, Eustigmatophyceae, Pinguiophyceae and Picophagea (also known as Synchromophyceae). Both clades, SI and SII, compose the Chrysista lineage. The remaining classes are grouped within the sister lineage Diatomista, equivalent to the SIII lineage; these are the diatoms or Bacillariophyceae, Bolidophyceae, Dictyochophyceae (including the silicoflagellates) and Pelagophyceae. A new class of algae, Olisthodiscophyceae, was described in 2021 and recovered as part of the SII lineage.

One group of heterotrophic heliozoan protists, Actinophryida, is included in some classifications as the sister lineage to the raphidophytes, and both groups are treated as one class Raphidomonadea on the basis of 18S rDNA phylogenetic analyses. However, a recent phylogenomic study places one actinophryid, Actinophrys sol, as the probable sister group to ochrophytes. Although it lacks chloroplasts, plastidial genes have been found in the nuclear genome of this actinophryid, implying that its common ancestor with ochrophytes may have already begun domesticating plastids.

Taxonomic history
In hierarchical classifications, where taxonomic ranks (kingdom, phylum, class, order...) are utilized, the heterokont algae are commonly regarded as an entire phylum (or division in botanical nomenclature) by the name of Ochrophyta, within the Stramenopila or Heterokonta. The phylum was first described by protozoologist Thomas Cavalier-Smith in 1986, as Ochrista, later renamed to Ochrophyta in 1996 in accordance to recommendations of the International Code of Nomenclature for algae, fungi, and plants (ICN). It remained a phylum-level taxon until 2017, when the same author lowered it to subphylum level and modified the name to Ochrophytina to match the -phytina suffix in botanical nomenclature, which corresponds to subdivisions. The phylum to which ochrophytes belong in his classification system is Gyrista, a clade that also contains some heterotrophic heterokonts, namely the Pseudofungi and the Bigyromonada. Gyrista and Bigyra compose the two main branches of stramenopiles, which are regarded as the superphylum Heterokonta within the kingdom Chromista. However, this classification system is in disuse due to the kingdom's non-monophyletic nature.

While Ochrophyta is the preferred name by general protistologists and protozoologists, the name Heterokontophyta is considered more familiar among phycologists. The origin of this name is the class Heterokontæ, introduced by Finnish biologist Alexander Ferdinand Luther in 1899 to include the orders Chloromonadales and Confervales, later separated into Xanthophyceae and Raphidophyceae. This name referenced, among other traits, the two unequal flagella characteristic of all Stramenopiles, also known as heterokonts. After several electron microscopy discoveries, Christiaan van den Hoek introduced in 1978 the division Heterokontophyta for five algal classes: Chrysophyceae, Xanthophyceae, Bacillariophyceae, Phaeophyceae, and Chloromonadophyceae. Several other names were used to group heterokont algae with ambiregnal organisms, such as Chromophyta, Heterokonta and lastly Stramenopiles, which is not a validly published name under the ICN. Several phycologists currently advocate the use of Heterokontophyta as the phylum name for heterokont algae. However, the original use by Hoek in 1978 did not provide a Latin description, which was a requirement for valid publication under the ICN until 2011. Phycologists Michael Guiry, Øjvind Moestrup and Robert Andersen validly published Heterokontophyta as a phylum in 2023.

As opposed to the hierarchical classification, the cladistic classification only recognizes clades as valid groups, rejecting the use of paraphyletic or polyphyletic groups. This method of classification is preferred among protistologists. The latest revision of the International Society of Protistologists, in 2019, recognizes Ochrophyta as a valid taxon within the higher Stramenopiles group, within the SAR supergroup. The subdivision of ochrophytes between Chrysista and Diatomista is fully accepted by the scientific community and backed up by phylogenetic analyses.

Classification
As of 2024, ochrophytes amount to 23,314 described species, with 490 species of uncertain position. However, it is estimated that they amount to more than 100,000 species, of which the majority are diatoms. Below is the present classification of ochrophytes according to the 2019 revision of eukaryotic classification, with the inclusion of classes of algae described in posterior years  as well as the number of described species for each class. According to the aforementioned 2019 revision by protistologists, the diatoms (Diatomeae) do not form a single class Bacillariophyceae, but numerous classes to reflect the phylogenetic advances over the previous decade.




 * Chrysista
 * Aurearenophyceae – 1 sp.
 * Chrysoparadoxophyceae – 1 sp.
 * Chrysophyceae – 1,274 spp.
 * Eustigmatophyceae – 218 spp.
 * Olisthodiscophyceae – 2 spp.
 * Phaeophyceae – 2,124 spp.
 * Phaeosacciophyceae – 8 spp.
 * Phaeothamniophyceae – 31 spp.
 * Raphidophyceae – 58 spp.
 * Schizocladiophyceae – 1 sp.
 * Xanthophyceae (=Heterokontae ; Heteromonadea ; Tribophyceae ) – 616 spp.
 * Diatomista
 * Dictyochophyceae – 217 spp.
 * Pelagophyceae –31 spp.
 * Pinguiophyceae – 5 spp.
 * Bolidophyceae – 18 spp.
 * Diatomeae (=Bacillariophyta ) – 14,684 spp.
 * Leptocylindrophytina
 * Leptocylindrophyceae
 * Corethrophyceae
 * Ellerbeckiophytina
 * Probosciophytina
 * Melosirophytina
 * Coscinodiscophytina
 * Rhizosoleniophytina
 * Arachnoidiscophytina
 * Bacillariophytina
 * Mediophyceae
 * Biddulphiophyceae
 * Bacillariophyceae

History of knowledge
Multicellular seaweeds, in the class Phaeophyceae, were described in early Chinese (around 3000 BC), Greek (300 BC, such as Theophrastus) and Japanese (ca. 500 AD) writings. Knowledge of them likely predates recorded history, being used as food, dyes, and for medicinal purposes. The first formal description of a stramenopile alga was that of the genus Fucus, by Linnaeus in his 1753 work Species Plantarum. Shortly after, unicellular chrysophytes were described by Otto Friedrich Müller. During this first era of scientific discovery, brown algae were described as plants, while microscopic algae were treated as animals under the name of infusoria.

During the 20th century, evolutionary and phylogenetic discussions began including heterokont algae. Transmission electron microscopy and molecular phylogenetic analysis led to the description of many new groups and several classes well into the 21st century. The sequencing of the first ochrophyte genome, belonging to Thalassiosira pseudonana, began in 2002.