Ochrophyte

Throughout history, different names have been used to describe photosynthetic stramenopiles. The more widely used name is the phylum —or division, in botanical nomenclature— Ochrophyta, This name was first coined by evolutionary biologist Thomas Cavalier-Smith in 1986 as Ochrista, The origin of this name is the class Heterokontæ (), introduced by Finnish biologist in 1899 to include yellow-green freshwater algae, now part of Xanthophyceae and Raphidophyceae. This name referenced, among other traits, the two unequal flagella characteristic of all stramenopiles, also known as heterokonts. Eventually it was expanded to include more algae and became the division Heterokontophyta, coined by Christiaan van den Hoek in 1978 and used to describe all photosynthetic stramenopiles. == Characteristics ==

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 (brown algae, seaweeds) develop as large multicellular thalli with differentiated tissues. 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. The two outer layers of ochrophyte plastids are contiguous 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. == Diversity ==

According to a 2024 survey, photosynthetic stramenopiles include 23,314 described species, with 490 species of uncertain position. • Chrysoparadoxophyceae – One enigmatic species of sand-dwelling unicellular algae, Chrysoparadoxa australica. Cells have been observed covered in cell walls, from which they escape as naked zoospores instead of dividing. They are exceptional for only having two chloroplast membranes. Cells may be naked or covered by cell walls, organic loricas, scales made of organic or siliceous material, or even be embedded in mucilage. • Phaeophyceae – Commonly known as brown algae, they are the second most species-rich group, with 2,124 primarily marine species. • Phaeosacciophyceae – Eight species • Raphidophyceae – 58 species • Schizocladiophyceae – One species of filamentous alga, Schizocladia ischiensis. It is similar to the filamentous Phaeophyceae, but distinguished by the absence of cellulose in its cell wall, and the absence of intercellular cytoplasmic connections. • Synchromophyceae – Five species of marine unicellular algae without flagella, that can join to form meroplasmodia. Some are colorless. One genus, Synchroma, has unique chloroplast complexes. • Xanthophyceae – 616 species of algae with an unusual yellow-green coloration. Some are macroscopic, either filamentous or siphonous, while others are single-celled and coccoid. == 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. 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. == Evolution ==

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. 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. Later, a 2025 study recovered A. sol within the SII clade instead, implying that, much like the Picophagea, it evolved from ochrophytes that secondarily lost their chloroplasts. == History of knowledge ==

Pre-Linnean The first recorded stramenopile algae in history were the multicellular brown algae, such as kelp and other seaweeds. Their descriptions date back to early China (ca. 3000 BC), Japan (ca. 500 BC) and Greece (300 BC, such as Theophrastus). Knowledge of them likely predates recorded history, as they were potentially used by humans as a source for food, dyes, and medicine. The remaining stramenopile algae were not included in historical works, due to being microscopic. In the late 17th century, Antony van Leeuwenhoek became the first person to observe microbes, but he did not record microscopic stramenopiles. The first unmistakeable descriptions of diatoms belong to two illustrations published anonymously in England in 1703, 80 years before the first taxonomic description of a diatom. They are attributed to Charles King of Staffordshire. Discovery period (1753–1882) The first formal description of any stramenopile was by Carl Linnaeus in his 1753 work Species Plantarum, for the brown alga Fucus. In the following years, single-celled chrysophytes and diatoms were described for the first time by Otto Friedrich Müller. These descriptions started a century-long era of exploration, during which brown algae were described as plants, while microscopic algae were treated as animals under the name of infusoria. One of the most significant contributions was the 1838 publication by Christian Gottfried Ehrenberg, containing his observations of many stramenopiles under light microscopy. was the first to hypothesize an evolutionary link between the diatoms, golden algae, and brown algae. Several authors later developed this idea through various publications, such as Carl Correns, Georg Klebs, and Ernst Lemmermann, and phylogenetic relationships between very different algal groups were discussed. In 1914, Adolf Pascher published a synthesis where he did not fully accept the evolutionary relationships between stramenopile algae. Pascher instead separated the Chrysophyta (including golden algae, xanthophytes and diatoms) and the Phaeophyta (brown algae alone). Floristic period (1914–1950) During the following period, evolutionary discussions were mostly abandoned, because characters observed under light microscopy were insufficient to resolve evolutionary relationships. But many species were described. 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. ==Notes==