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A diatom (
Neo-Latin New Latin (also called Neo-Latin or Modern Latin) is the revival of Literary Latin used in original, scholarly, and scientific works since about 1500. Modern scholarly and technical nomenclature, such as in zoological and botanical taxonomy ...
''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group comprising several
genera Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclat ...
of
algae Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular micr ...
, specifically
microalgae Microalgae or microphytes are microscopic algae invisible to the naked eye. They are phytoplankton typically found in freshwater and marine systems, living in both the water column and sediment. They are unicellular species which exist indiv ...
, found in the oceans, waterways and soils of the world. Living diatoms make up a significant portion of the Earth's
biomass Biomass is plant-based material used as a fuel for heat or electricity production. It can be in the form of wood, wood residues, energy crops, agricultural residues, and waste from industry, farms, and households. Some people use the terms bio ...
: they generate about 20 to 50 percent of the
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...
produced on the planet each year, take in over 6.7 billion metric tons of
silicon Silicon is a chemical element with the symbol Si and atomic number 14. It is a hard, brittle crystalline solid with a blue-grey metallic luster, and is a tetravalent metalloid and semiconductor. It is a member of group 14 in the periodic ...
each year from the waters in which they live, and constitute nearly half of the organic material found in the oceans. The shells of dead diatoms can reach as much as a half-mile (800 m) deep on the ocean floor, and the entire
Amazon basin The Amazon basin is the part of South America drained by the Amazon River and its tributaries. The Amazon drainage basin covers an area of about , or about 35.5 percent of the South American continent. It is located in the countries of Boli ...
is fertilized annually by 27 million tons of diatom shell dust transported by transatlantic winds from the African
Sahara , photo = Sahara real color.jpg , photo_caption = The Sahara taken by Apollo 17 astronauts, 1972 , map = , map_image = , location = , country = , country1 = , ...
, much of it from the
Bodélé Depression The Bodélé Depression (), located at the southern edge of the Sahara Desert in north central Africa, is the lowest point in Chad. It is 500 km long, 150 km wide and around 160 m deep. Its bottom lies about 155 meters above sea leve ...
, which was once made up of a system of fresh-water lakes. Diatoms are
unicellular organism A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms a ...
s: they occur either as solitary cells or in
colonies In modern parlance, a colony is a territory subject to a form of foreign rule. Though dominated by the foreign colonizers, colonies remain separate from the administration of the original country of the colonizers, the '' metropolitan state'' ...
, which can take the shape of ribbons, fans, zigzags, or stars. Individual cells range in size from 2 to 200 micrometers. In the presence of adequate nutrients and sunlight, an assemblage of living diatoms doubles approximately every 24 hours by asexual
multiple fission Fission, in biology, is the division of a single entity into two or more parts and the regeneration of those parts to separate entities resembling the original. The object experiencing fission is usually a cell, but the term may also refer to how ...
; the maximum life span of individual cells is about six days. Diatoms have two distinct shapes: a few (''centric diatoms'') are ''radially'' symmetric, while most (''pennate diatoms'') are broadly ''bilaterally'' symmetric. A unique feature of diatom
anatomy Anatomy () is the branch of biology concerned with the study of the structure of organisms and their parts. Anatomy is a branch of natural science that deals with the structural organization of living things. It is an old science, having i ...
is that they are surrounded by a
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mec ...
made of silica (hydrated
silicon dioxide Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is one ...
), called a
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
. These frustules have
structural coloration Structural coloration in animals, and a few plants, is the production of colour by microscopically structured surfaces fine enough to interfere with visible light instead of pigments, although some structural coloration occurs in combination wi ...
due to their
photonic Photonics is a branch of optics that involves the application of generation, detection, and manipulation of light in form of photons through emission, transmission, modulation, signal processing, switching, amplification, and sensing. Though ...
nanostructure A nanostructure is a structure of intermediate size between microscopic and molecular structures. Nanostructural detail is microstructure at nanoscale. In describing nanostructures, it is necessary to differentiate between the number of dimens ...
, prompting them to be described as "jewels of the sea" and "living opals". Movement in diatoms primarily occurs passively as a result of both
ocean current An ocean current is a continuous, directed movement of sea water generated by a number of forces acting upon the water, including wind, the Coriolis effect, breaking waves, cabbeling, and temperature and salinity differences. Depth conto ...
s and wind-induced water
turbulence In fluid dynamics, turbulence or turbulent flow is fluid motion characterized by chaotic changes in pressure and flow velocity. It is in contrast to a laminar flow, which occurs when a fluid flows in parallel layers, with no disruption between ...
; however, male
gamete A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
s of centric diatoms have
flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have fro ...
, permitting active movement to seek female gametes. Similar to
plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae excl ...
s, diatoms convert
light energy Light or visible light is electromagnetic radiation that can be perceived by the human eye. Visible light is usually defined as having wavelengths in the range of 400–700 nanometres (nm), corresponding to frequencies of 750–420 terahe ...
to
chemical energy Chemical energy is the energy of chemical substances that is released when they undergo a chemical reaction and transform into other substances. Some examples of storage media of chemical energy include batteries, Schmidt-Rohr, K. (2018). "How ...
by
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...
, but their chloroplasts were acquired in different ways. Unusually for autotrophic organisms, diatoms possess a
urea cycle The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions that produces urea (NH2)2CO from ammonia (NH3). Animals that use this cycle, mainly amphibians and mammals, are called ureotelic. The urea cycle converts h ...
, a feature that they share with
animal Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage ...
s, although this cycle is used to different metabolic ends in diatoms. The family ''Rhopalodiaceae'' also possess a
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
l
endosymbiont An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
called a spheroid body. This endosymbiont has lost its photosynthetic properties, but has kept its ability to perform
nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...
, allowing the diatom to fix atmospheric nitrogen. Other diatoms in symbiosis with nitrogen-fixing cyanobacteria are among the genera ''Hemiaulus'', ''Rhizosolenia'' and ''Chaetoceros''. Dinotoms are diatoms that have become endosymbionts inside dinoflagellates. Research on the dinoflagellates ''Durinskia baltica'' and ''Glenodinium foliaceum'' have shown that the endosymbiont event happened so recently, evolutionarily speaking, that their organelles and genome are still intact with minimum to no gene loss. The main difference between these and free living diatoms is that they have lost their cell wall of silica, making them the only known shell-less diatoms. The study of diatoms is a branch of
phycology Phycology () is the scientific study of algae. Also known as algology, phycology is a branch of life science. Algae are important as primary producers in aquatic ecosystems. Most algae are eukaryotic, photosynthetic organisms that live in a ...
. Diatoms are classified as
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
s, organisms with a
nuclear envelope The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material. The nuclear envelope consists of two lipid bilayer membr ...
-bound
cell nucleus The cell nucleus (pl. nuclei; from Latin or , meaning ''kernel'' or ''seed'') is a membrane-bound organelle found in eukaryotic cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, h ...
, that separates them from the
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
s
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
and
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
. Diatoms are a type of
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
called
phytoplankton Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater ecosystems. The name comes from the Greek words (), meaning 'plant', and (), meaning 'wanderer' or 'drifter'. ...
, the most common of the plankton types. Diatoms also grow attached to
benthic The benthic zone is the ecological region at the lowest level of a body of water such as an ocean, lake, or stream, including the sediment surface and some sub-surface layers. The name comes from ancient Greek, βένθος (bénthos), meaning " ...
substrates, floating debris, and on macrophytes. They comprise an integral component of the
periphyton Periphyton is a complex mixture of algae, cyanobacteria, heterotrophic microbes, and detritus that is attached to submerged surfaces in most aquatic ecosystems. The related term Aufwuchs (German "surface growth" or "overgrowth") refers to the col ...
community. Another classification divides plankton into eight types based on size: in this scheme, diatoms are classed as microalgae. Several systems for classifying the individual diatom
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriat ...
exist.
Fossil A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...
evidence suggests that diatoms originated during or before the early
Jurassic The Jurassic ( ) is a geologic period and stratigraphic system that spanned from the end of the Triassic Period million years ago (Mya) to the beginning of the Cretaceous Period, approximately Mya. The Jurassic constitutes the middle period of ...
period, which was about 150 to 200 million years ago. The oldest fossil evidence for diatoms is a specimen of extant genus ''Hemiaulus'' in Late Jurassic aged amber from Thailand. Diatoms are used to monitor past and present environmental conditions, and are commonly used in studies of water quality.
Diatomaceous earth Diatomaceous earth (), diatomite (), or kieselgur/kieselguhr is a naturally occurring, soft, siliceous sedimentary rock that can be crumbled into a fine white to off-white powder. It has a particle size ranging from more than 3 μm to l ...
(diatomite) is a collection of diatom shells found in the earth's crust. They are soft, silica-containing sedimentary rocks which are easily crumbled into a fine powder and typically have a particle size of 10 to 200 μm. Diatomaceous earth is used for a variety of purposes including for water filtration, as a mild abrasive, in cat litter, and as a dynamite stabilizer.


Overview

Diatoms are protists that form massive annual spring and fall blooms in aquatic environments and are estimated to be responsible for about half of photosynthesis in the global oceans. This predictable annual bloom dynamic fuels higher trophic levels and initiates delivery of carbon into the deep ocean biome. Diatoms have complex life history strategies that are presumed to have contributed to their rapid genetic diversification into ~200,000 species that are distributed between the two major diatom groups: centrics and pennates. Modified material was copied from this source, which is available under
Creative Commons Attribution 4.0 International License


Morphology

Diatoms are generally 2 to 200 micrometers in size, with a few larger species. Their yellowish-brown
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it i ...
s, the site of photosynthesis, are typical of
heterokont Heterokonts are a group of protists (formally referred to as Heterokonta, Heterokontae or Heterokontophyta). The group is a major line of eukaryotes. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms, which a ...
s, having four
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment (t ...
s and containing
pigments A pigment is a colored material that is completely or nearly insoluble in water. In contrast, dyes are typically soluble, at least at some stage in their use. Generally dyes are often organic compounds whereas pigments are often inorganic compoun ...
such as the
carotenoid Carotenoids (), also called tetraterpenoids, are yellow, orange, and red organic pigments that are produced by plants and algae, as well as several bacteria, and fungi. Carotenoids give the characteristic color to pumpkins, carrots, parsnips, ...
fucoxanthin. Individuals usually lack
flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have fro ...
, but they are present in male
gamete A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
s of the centric diatoms and have the usual heterokont structure, including the hairs (
mastigoneme Mastigonemes are lateral "hairs" that attach to protistan flagella. Flimsy hairs attach to the flagella of euglenid flagellates, while stiff hairs occur in stramenopile and cryptophyte protists.Hoek, C. van den, Mann, D. G. and Jahns, H. ...
s) characteristic in other groups. Diatoms are often referred as "jewels of the sea" or "living opals" due to their optical properties. The biological function of this
structural coloration Structural coloration in animals, and a few plants, is the production of colour by microscopically structured surfaces fine enough to interfere with visible light instead of pigments, although some structural coloration occurs in combination wi ...
is not clear, but it is speculated that it may be related to communication, camouflage, thermal exchange and/or UV protection. Diatoms build intricate hard but porous cell walls called
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
s composed primarily of
silica Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is ...
. This siliceous wall can be highly patterned with a variety of pores, ribs, minute spines, marginal ridges and elevations; all of which can be used to delineate genera and species. The cell itself consists of two halves, each containing an essentially flat plate, or valve, and marginal connecting, or girdle band. One half, the ''hypotheca'', is slightly smaller than the other half, the ''epitheca''. Diatom morphology varies. Although the shape of the cell is typically circular, some cells may be triangular, square, or elliptical. Their distinguishing feature is a hard mineral shell or frustule composed of opal (hydrated, polymerized silicic acid). Diatoms are divided into two groups that are distinguished by the shape of the frustule: the ''centric diatoms'' and the ''pennate diatoms''. Pennate diatoms are bilaterally symmetric. Each one of their valves have openings that are slits along the
raphe Raphe (; from Greek ῥαφή, "seam"Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon. revised and augmented throughout by Sir Henry Stuart Jones. with the assistance of. Roderick McKenzie.'' Oxford: Clarendon Press.) has several diffe ...
s and their shells are typically elongated parallel to these raphes. They generate cell movement through cytoplasm that streams along the raphes, always moving along solid surfaces. Centric diatoms are radially symmetric. They are composed of upper and lower valves – ''epitheca'' and ''hypotheca'' – each consisting of a valve and a girdle band that can easily slide underneath each other and expand to increase cell content over the diatoms progression. The cytoplasm of the centric diatom is located along the inner surface of the shell and provides a hollow lining around the large vacuole located in the center of the cell. This large, central vacuole is filled by a fluid known as "cell sap" which is similar to seawater but varies with specific ion content. The cytoplasmic layer is home to several organelles, like the chloroplasts and mitochondria. Before the centric diatom begins to expand, its nucleus is at the center of one of the valves and begins to move towards the center of the cytoplasmic layer before division is complete. Centric diatoms have a variety of shapes and sizes, depending on from which axis the shell extends, and if spines are present.


Silicification

Diatom cells are contained within a unique silica
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mec ...
known as a
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
made up of two valves called
theca In biology, a theca (plural thecae) is a sheath or a covering. Botany In botany, the theca is related to plant's flower anatomy. The theca of an angiosperm consists of a pair of microsporangia that are adjacent to each other and share a comm ...
e, that typically overlap one another. The
biogenic silica Biogenic silica (bSi), also referred to as opal, biogenic opal, or amorphous opaline silica, forms one of the most widespread biogenic minerals. For example, microscopic particles of silica called phytoliths can be found in grasses and other plant ...
composing the cell wall is synthesised
intracellular This glossary of biology terms is a list of definitions of fundamental terms and concepts used in biology, the study of life and of living organisms. It is intended as introductory material for novices; for more specific and technical definitions ...
ly by the
polymerisation In polymer chemistry, polymerization (American English), or polymerisation (British English), is a process of reacting monomer molecules together in a chemical reaction to form polymer chains or three-dimensional networks. There are many for ...
of
silicic acid Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is one ...
monomer In chemistry, a monomer ( ; '' mono-'', "one" + '' -mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or three-dimensional network in a process called polymerization. Classification ...
s. This material is then extruded to the cell exterior and added to the wall. In most species, when a diatom divides to produce two daughter cells, each cell keeps one of the two-halves and grows a smaller half within it. As a result, after each division cycle, the average size of diatom cells in the population gets smaller. Once such cells reach a certain minimum size, rather than simply divide, they reverse this decline by forming an
auxospore In certain species of diatoms, auxospores are specialised cells that are produced at key stages in their cell cycle or life history. Auxospores typically play a role in growth processes, sexual reproduction or dormancy.Hoek, C. van den, Mann, D ...
. This expands in size to give rise to a much larger cell, which then returns to size-diminishing divisions. Auxospore production is almost always linked to
meiosis Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately ...
and sexual reproduction. The exact mechanism of transferring
silica Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is ...
absorbed by the diatom to the
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mec ...
is unknown. Much of the sequencing of diatom genes comes from the search for the mechanism of silica uptake and deposition in nano-scale patterns in the
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
. The most success in this area has come from two species, '' Thalassiosira pseudonana'', which has become the model species, as the whole genome was sequenced and methods for genetic control were established, and ''Cylindrotheca fusiformis'', in which the important silica deposition proteins silaffins were first discovered. Silaffins, sets of polycationic
peptides Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. ...
, were found in ''C. fusiformis'' cell walls and can generate intricate silica structures. These structures demonstrated pores of sizes characteristic to diatom patterns. When ''T. pseudonana'' underwent genome analysis it was found that it encoded a
urea cycle The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions that produces urea (NH2)2CO from ammonia (NH3). Animals that use this cycle, mainly amphibians and mammals, are called ureotelic. The urea cycle converts h ...
, including a higher number of
polyamines A polyamine is an organic compound having more than two amino groups. Alkyl polyamines occur naturally, but some are synthetic. Alkylpolyamines are colorless, hygroscopic, and water soluble. Near neutral pH, they exist as the ammonium derivatives. ...
than most genomes, as well as three distinct silica transport genes. In a
phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
study on silica transport genes from 8 diverse groups of diatoms, silica transport was found to generally group with species. This study also found structural differences between the silica transporters of pennate (bilateral symmetry) and centric (radial symmetry) diatoms. The sequences compared in this study were used to create a diverse background in order to identify residues that differentiate function in the silica deposition process. Additionally, the same study found that a number of the regions were conserved within species, likely the base structure of silica transport. These silica transport proteins are unique to diatoms, with no
homologs A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization. Homologs have the same genes in the same loci where they provide points alon ...
found in other species, such as sponges or rice. The divergence of these silica transport genes is also indicative of the structure of the protein evolving from two repeated units composed of five membrane bound segments, which indicates either gene duplication or
dimerization A dimer () ('' di-'', "two" + ''-mer'', "parts") is an oligomer consisting of two monomers joined by bonds that can be either strong or weak, covalent or intermolecular. Dimers also have significant implications in polymer chemistry, inorganic che ...
. The silica deposition that takes place from the membrane bound vesicle in diatoms has been hypothesized to be a result of the activity of silaffins and long chain polyamines. This Silica Deposition Vesicle (SDV) has been characterized as an acidic compartment fused with Golgi-derived vesicles. These two protein structures have been shown to create sheets of patterned silica
in-vivo Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and pl ...
with irregular pores on the scale of diatom frustules. One hypothesis as to how these proteins work to create complex structure is that residues are conserved within the SDV's, which is unfortunately difficult to identify or observe due to the limited number of diverse sequences available. Though the exact mechanism of the highly uniform deposition of silica is as yet unknown, the ''Thalassiosira pseudonana'' genes linked to silaffins are being looked to as targets for genetic control of nanoscale silica deposition. The ability of diatoms to make silica-based
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mec ...
s has been the subject of fascination for centuries. It started with a microscopic observation by an anonymous English country nobleman in 1703, who observed an object that looked like a chain of regular parallelograms and debated whether it was just crystals of salt, or a plant. The viewer decided that it was a plant because the parallelograms didn't separate upon agitation, nor did they vary in appearance when dried or subjected to warm water (in an attempt to dissolve the "salt"). Unknowingly, the viewer's confusion captured the essence of diatoms—mineral utilizing plants. It is not clear when it was determined that diatom cell walls are made of silica, but in 1939 a seminal reference characterized the material as
silicic acid Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is one ...
in a "subcolloidal" state Identification of the main chemical component of the cell wall spurred investigations into how it was made. These investigations have involved, and been propelled by, diverse approaches including, microscopy, chemistry, biochemistry,
material characterisation Characterization, when used in materials science, refers to the broad and general process by which a material's structure and properties are probed and measured. It is a fundamental process in the field of materials science, without which no scie ...
,
molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and phys ...
,
'omics The branches of science known informally as omics are various disciplines in biology whose names end in the suffix '' -omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collec ...
, and
transgenic A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis, has the potential to change the ...
approaches. The results from this work have given a better understanding of cell wall formation processes, establishing fundamental knowledge which can be used to create models that contextualise current findings and clarify how the process works. Modified material was copied from this source, which is available under
Creative Commons Attribution 4.0 International License
The process of building a mineral-based cell wall inside the cell, then exporting it outside, is a massive event that must involve large numbers of genes and their protein products. The act of building and
exocytosing Exocytosis () is a form of active transport and bulk transport in which a cell transports molecules (e.g., neurotransmitters and proteins) out of the cell ('' exo-'' + ''cytosis''). As an active transport mechanism, exocytosis requires the use o ...
this large structural object in a short time period, synched with
cell cycle The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and sub ...
progression, necessitates substantial physical movements within the cell as well as dedication of a significant proportion of the cell's
biosynthetic Biosynthesis is a multi-step, enzyme-Catalysis, catalyzed process where substrate (chemistry), substrates are converted into more complex Product (chemistry), products in living organisms. In biosynthesis, simple Chemical compound, compounds are mo ...
capacities. The first characterisations of the biochemical processes and components involved in diatom silicification were made in the late 1990s. These were followed by insights into how higher order assembly of silica structures might occur. More recent reports describe the identification of novel components involved in higher order processes, the dynamics documented through real-time imaging, and the genetic manipulation of silica structure. The approaches established in these recent works provide practical avenues to not only identify the components involved in silica cell wall formation but to elucidate their interactions and spatio-temporal dynamics. This type of holistic understanding will be necessary to achieve a more complete understanding of cell wall synthesis.


Behaviour

Most centric and araphid pennate diatoms are nonmotile, and their relatively dense cell walls cause them to readily sink.
Plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
ic forms in open water usually rely on
turbulent In fluid dynamics, turbulence or turbulent flow is fluid motion characterized by chaotic changes in pressure and flow velocity. It is in contrast to a laminar flow, which occurs when a fluid flows in parallel layers, with no disruption between ...
mixing of the upper layers of the oceanic waters by the wind to keep them suspended in sunlit surface waters. Many planktonic diatoms have also evolved features that slow their sinking rate, such as spines or the ability to grow in colonial chains. These adaptations increase their surface area to volume ratio and drag, allowing them to stay suspended in the water column longer. Individual cells may regulate
buoyancy Buoyancy (), or upthrust, is an upward force exerted by a fluid that opposes the weight of a partially or fully immersed object. In a column of fluid, pressure increases with depth as a result of the weight of the overlying fluid. Thus the ...
via an ionic pump. Some pennate diatoms are capable of a type of locomotion called "gliding", which allows them to move across surfaces via adhesive
mucilage Mucilage is a thick, gluey substance produced by nearly all plants and some microorganisms. These microorganisms include protists which use it for their locomotion. The direction of their movement is always opposite to that of the secretion of m ...
secreted through a seamlike structure called the raphe. In order for a diatom cell to glide, it must have a solid substrate for the mucilage to adhere to. Cells are solitary or united into colonies of various kinds, which may be linked by siliceous structures;
mucilage Mucilage is a thick, gluey substance produced by nearly all plants and some microorganisms. These microorganisms include protists which use it for their locomotion. The direction of their movement is always opposite to that of the secretion of m ...
pads, stalks or tubes; amorphous masses of mucilage; or by threads of
chitin Chitin ( C8 H13 O5 N)n ( ) is a long-chain polymer of ''N''-acetylglucosamine, an amide derivative of glucose. Chitin is probably the second most abundant polysaccharide in nature (behind only cellulose); an estimated 1 billion tons of chit ...
(polysaccharide), which are secreted through strutted processes of the cell.


Life cycle


Reproduction and cell size

Reproduction among these organisms is asexual by
binary fission Binary may refer to: Science and technology Mathematics * Binary number, a representation of numbers using only two digits (0 and 1) * Binary function, a function that takes two arguments * Binary operation, a mathematical operation that ta ...
, during which the diatom divides into two parts, producing two "new" diatoms with identical genes. Each new organism receives one of the two
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
s – one larger, the other smaller – possessed by the parent, which is now called the epitheca; and is used to construct a second, smaller frustule, the hypotheca. The diatom that received the larger frustule becomes the same size as its parent, but the diatom that received the smaller frustule remains smaller than its parent. This causes the average cell size of this diatom population to decrease. It has been observed, however, that certain taxa have the ability to divide without causing a reduction in cell size. Nonetheless, in order to restore the cell size of a diatom population for those that do endure size reduction, sexual reproduction and
auxospore In certain species of diatoms, auxospores are specialised cells that are produced at key stages in their cell cycle or life history. Auxospores typically play a role in growth processes, sexual reproduction or dormancy.Hoek, C. van den, Mann, D ...
formation must occur.


Cell division

Vegetative cells of diatoms are
diploid Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectiv ...
(2N) and so
meiosis Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately ...
can take place, producing male and female gametes which then fuse to form the
zygote A zygote (, ) is a eukaryotic cell formed by a fertilization event between two gametes. The zygote's genome is a combination of the DNA in each gamete, and contains all of the genetic information of a new individual organism. In multicell ...
. The zygote sheds its silica theca and grows into a large sphere covered by an organic membrane, the auxospore. A new diatom cell of maximum size, the initial cell, forms within the auxospore thus beginning a new generation. Resting spores may also be formed as a response to unfavourable environmental conditions with germination occurring when conditions improve. A defining characteristic of all diatoms is their restrictive and bipartite silica cell wall that causes them to progressively shrink during asexual cell division. At a critically small cell size and under certain conditions,
auxosporulation In certain species of diatoms, auxospores are specialised cells that are produced at key stages in their cell cycle or life history. Auxospores typically play a role in growth processes, sexual reproduction or dormancy.Hoek, C. van den, Mann, D ...
restitutes cell size and prevents clonal death. The entire lifecycles of only a few diatoms have been described and rarely have sexual events been captured in the environment.


Sperm motility

Diatoms are mostly non-motile; however, sperm found in some species can be
flagellated A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide Motility#Cellular level, motility. Many protists with flagella are termed as flagellates. A m ...
, though motility is usually limited to a gliding motion. In centric diatoms, the small male
gametes A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
have one
flagellum A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f ...
while the female gametes are large and non-motile ( oogamous). Conversely, in pennate diatoms both gametes lack flagella ( isogamous). Certain araphid species, that is pennate diatoms without a
raphe Raphe (; from Greek ῥαφή, "seam"Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon. revised and augmented throughout by Sir Henry Stuart Jones. with the assistance of. Roderick McKenzie.'' Oxford: Clarendon Press.) has several diffe ...
(seam), have been documented as anisogamous and are, therefore, considered to represent a transitional stage between centric and raphid pennate diatoms, diatoms with a raphe.


Degradation by microbes

Certain species of bacteria in oceans and lakes can accelerate the rate of dissolution of silica in dead and living diatoms by using
hydrolytic Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile. Biological hydrolysis i ...
enzymes to break down the organic algal material.


Ecology


Distribution

Diatoms are a widespread group and can be found in the
ocean The ocean (also the sea or the world ocean) is the body of salt water that covers approximately 70.8% of the surface of Earth and contains 97% of Earth's water. An ocean can also refer to any of the large bodies of water into which the wor ...
s, in
fresh water Fresh water or freshwater is any naturally occurring liquid or frozen water containing low concentrations of dissolved salts and other total dissolved solids. Although the term specifically excludes seawater and brackish water, it does incl ...
, in
soil Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Some scientific definitions distinguish ''dirt'' from ''soil'' by restricting the former ...
s, and on damp surfaces. They are one of the dominant components of
phytoplankton Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater ecosystems. The name comes from the Greek words (), meaning 'plant', and (), meaning 'wanderer' or 'drifter'. ...
in nutrient-rich coastal waters and during oceanic spring blooms, since they can divide more rapidly than other groups of phytoplankton. Most live
pelagic The pelagic zone consists of the water column of the open ocean, and can be further divided into regions by depth (as illustrated on the right). The word ''pelagic'' is derived . The pelagic zone can be thought of as an imaginary cylinder or w ...
ally in open water, although some live as surface films at the water-sediment interface (
benthic The benthic zone is the ecological region at the lowest level of a body of water such as an ocean, lake, or stream, including the sediment surface and some sub-surface layers. The name comes from ancient Greek, βένθος (bénthos), meaning " ...
), or even under damp atmospheric conditions. They are especially important in oceans, where they contribute an estimated 45% of the total oceanic
primary production In ecology, primary production is the synthesis of organic compounds from atmospheric or aqueous carbon dioxide. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through ...
of organic material. Spatial distribution of marine phytoplankton species is restricted both horizontally and vertically.


Growth

Plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
ic diatoms in freshwater and marine environments typically exhibit a "
boom and bust Business cycles are intervals of expansion followed by recession in economic activity. These changes have implications for the welfare of the broad population as well as for private institutions. Typically business cycles are measured by examini ...
" (or "''bloom'' and bust") lifestyle. When conditions in the upper mixed layer (nutrients and light) are favourable (as at the
spring Spring(s) may refer to: Common uses * Spring (season), a season of the year * Spring (device), a mechanical device that stores energy * Spring (hydrology), a natural source of water * Spring (mathematics), a geometric surface in the shape of a h ...
), their competitive edge and rapid growth rate enables them to dominate phytoplankton communities ("boom" or "bloom"). As such they are often classed as opportunistic
r-strategists In ecology, ''r''/''K'' selection theory relates to the selection of combinations of traits in an organism that trade off between quantity and quality of offspring. The focus on either an increased quantity of offspring at the expense of individ ...
(''i.e.'' those organisms whose ecology is defined by a high growth rate, ''r'').


Impact

The freshwater diatom '' Didymosphenia geminata'', commonly known as ''Didymo,'' causes severe environmental degradation in water-courses where it blooms, producing large quantities of a brown jelly-like material called "brown snot" or "rock snot". This diatom is native to Europe and is an
invasive species An invasive species otherwise known as an alien is an introduced organism that becomes overpopulated and harms its new environment. Although most introduced species are neutral or beneficial with respect to other species, invasive species adv ...
both in the
antipodes In geography, the antipode () of any spot on Earth is the point on Earth's surface diametrically opposite to it. A pair of points ''antipodal'' () to each other are situated such that a straight line connecting the two would pass through ...
and in parts of
North America North America is a continent in the Northern Hemisphere and almost entirely within the Western Hemisphere. It is bordered to the north by the Arctic Ocean, to the east by the Atlantic Ocean, to the southeast by South America and th ...
. The problem is most frequently recorded from
Australia Australia, officially the Commonwealth of Australia, is a sovereign country comprising the mainland of the Australian continent, the island of Tasmania, and numerous smaller islands. With an area of , Australia is the largest country by ...
and
New Zealand New Zealand ( mi, Aotearoa ) is an island country in the southwestern Pacific Ocean. It consists of two main landmasses—the North Island () and the South Island ()—and over 700 smaller islands. It is the sixth-largest island coun ...
. When conditions turn unfavourable, usually upon depletion of nutrients, diatom cells typically increase in sinking rate and exit the upper mixed layer ("bust"). This sinking is induced by either a loss of buoyancy control, the synthesis of mucilage that sticks diatoms cells together, or the production of heavy ''resting spores''. Sinking out of the upper mixed layer removes diatoms from conditions unfavourable to growth, including grazer populations and higher temperatures (which would otherwise increase cell
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run ...
). Cells reaching deeper water or the shallow seafloor can then rest until conditions become more favourable again. In the open ocean, many sinking cells are lost to the deep, but refuge populations can persist near the
thermocline A thermocline (also known as the thermal layer or the metalimnion in lakes) is a thin but distinct layer in a large body of fluid (e.g. water, as in an ocean or lake; or air, e.g. an atmosphere) in which temperature changes more drastically with ...
. Ultimately, diatom cells in these resting populations re-enter the upper mixed layer when vertical mixing entrains them. In most circumstances, this mixing also replenishes nutrients in the upper mixed layer, setting the scene for the next round of diatom blooms. In the open ocean (away from areas of continuous
upwelling Upwelling is an physical oceanography, oceanographic phenomenon that involves wind-driven motion of dense, cooler, and usually nutrient-rich water from deep water towards the ocean surface. It replaces the warmer and usually nutrient-depleted ...
), this cycle of bloom, bust, then return to pre-bloom conditions typically occurs over an annual cycle, with diatoms only being prevalent during the spring and early summer. In some locations, however, an autumn bloom may occur, caused by the breakdown of summer stratification and the entrainment of nutrients while light levels are still sufficient for growth. Since vertical mixing is increasing, and light levels are falling as winter approaches, these blooms are smaller and shorter-lived than their spring equivalents. In the open ocean, the diatom (spring) bloom is typically ended by a shortage of silicon. Unlike other minerals, the requirement for silicon is unique to diatoms and it is not regenerated in the plankton ecosystem as efficiently as, for instance,
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
or
phosphorus Phosphorus is a chemical element with the symbol P and atomic number 15. Elemental phosphorus exists in two major forms, white phosphorus and red phosphorus, but because it is highly reactive, phosphorus is never found as a free element on Ea ...
nutrients. This can be seen in maps of surface nutrient concentrations – as nutrients decline along gradients, silicon is usually the first to be exhausted (followed normally by nitrogen then phosphorus). Because of this bloom-and-bust cycle, diatoms are believed to play a disproportionately important role in the export of carbon from oceanic surface waters (see also the
biological pump The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments.Sigman DM & GH ...
). Significantly, they also play a key role in the regulation of the
biogeochemical cycle A biogeochemical cycle (or more generally a cycle of matter) is the pathway by which a chemical substance cycles (is turned over or moves through) the biotic and the abiotic compartments of Earth. The biotic compartment is the biosphere and th ...
of
silicon Silicon is a chemical element with the symbol Si and atomic number 14. It is a hard, brittle crystalline solid with a blue-grey metallic luster, and is a tetravalent metalloid and semiconductor. It is a member of group 14 in the periodic ...
in the modern ocean.


Reason for success

Diatoms are ecologically successful, and occur in virtually every environment that contains water – not only oceans, seas, lakes, and streams, but also soil and wetlands. The use of silicon by diatoms is believed by many researchers to be the key to this ecological success. Raven (1983) noted that, relative to organic
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mec ...
s, silica frustules require less energy to synthesize (approximately 8% of a comparable organic wall), potentially a significant saving on the overall cell energy budget. In a now classic study, Egge and Aksnes (1992) found that diatom dominance of
mesocosm thumb , Diagram of a small form closed system mesocosm. A mesocosm (''meso-'' or 'medium' and ''-cosm'' 'world') is any outdoor experimental system that examines the natural environment under controlled conditions. In this way mesocosm studie ...
communities was directly related to the availability of silicic acid – when concentrations were greater than 2 μmol m−3, they found that diatoms typically represented more than 70% of the phytoplankton community. Other researchers have suggested that the biogenic silica in diatom cell walls acts as an effective pH
buffering agent A buffer solution (more precisely, pH buffer or hydrogen ion buffer) is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa. Its pH changes very little when a small amount of strong acid or base is ...
, facilitating the conversion of
bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial biochemi ...
to dissolved CO2 (which is more readily assimilated). More generally, notwithstanding these possible advantages conferred by their use of silicon, diatoms typically have higher growth rates than other algae of the same corresponding size.


Sources for collection

Diatoms can be obtained from multiple sources.Chamberlain, C. J. (1901) ''Methods in Plant Histology'', University of Chicago Press, USA Marine diatoms can be collected by direct water sampling, and benthic forms can be secured by scraping
barnacle A barnacle is a type of arthropod constituting the subclass Cirripedia in the subphylum Crustacea, and is hence related to crabs and lobsters. Barnacles are exclusively marine, and tend to live in shallow and tidal waters, typically in erosiv ...
s,
oyster Oyster is the common name for a number of different families of salt-water bivalve molluscs that live in marine or brackish habitats. In some species, the valves are highly calcified, and many are somewhat irregular in shape. Many, but not ...
and other shells. Diatoms are frequently present as a brown, slippery coating on submerged stones and sticks, and may be seen to "stream" with river current. The surface mud of a pond, ditch, or lagoon will almost always yield some diatoms. Living diatoms are often found clinging in great numbers to filamentous algae, or forming gelatinous masses on various submerged plants. ''
Cladophora ''Cladophora'' is a genus of reticulated filamentous Ulvophyceae (green algae). The genus ''Cladophora'' contains many species that are very hard to tell apart and classify, mainly because of the great variation in their appearances, which is a ...
'' is frequently covered with ''
Cocconeis ''Cocconeis'' is a genus of diatoms. Members of the genus are elliptically shaped diatoms. The green alga ''Cladophora'' is frequently covered with ''Cocconeis'', as are individuals of Antarctic minke whale The Antarctic minke whale or sout ...
'', an elliptically shaped diatom; ''
Vaucheria ''Vaucheria'' is a genus of Xanthophyceae or yellow-green algae known as water felt. It is one of only two genera in the family Vaucheriaceae. The type species of the genus is '' Vaucheria disperma''. The genus was circumscribed by Augustin Pyr ...
'' is often covered with small forms. Since diatoms form an important part of the food of
mollusc Mollusca is the second-largest phylum of invertebrate animals after the Arthropoda, the members of which are known as molluscs or mollusks (). Around 85,000  extant species of molluscs are recognized. The number of fossil species is est ...
s,
tunicate A tunicate is a marine invertebrate animal, a member of the subphylum Tunicata (). It is part of the Chordata, a phylum which includes all animals with dorsal nerve cords and notochords (including vertebrates). The subphylum was at one t ...
s, and
fish Fish are Aquatic animal, aquatic, craniate, gill-bearing animals that lack Limb (anatomy), limbs with Digit (anatomy), digits. Included in this definition are the living hagfish, lampreys, and Chondrichthyes, cartilaginous and bony fish as we ...
es, the
alimentary tract The gastrointestinal tract (GI tract, digestive tract, alimentary canal) is the tract or passageway of the digestive system that leads from the mouth to the anus. The GI tract contains all the major organs of the digestive system, in humans and ...
s of these animals often yield forms that are not easily secured in other ways. Diatoms can be made to emerge by filling a jar with water and mud, wrapping it in black paper and letting direct sunlight fall on the surface of the water. Within a day, the diatoms will come to the top in a scum and can be isolated.


Biogeochemistry

File:Oceanic Silicon Cycle Budget.svg, The modern oceanic silicon cycle
Fluxes are in T mol Si y−1 (28 million
metric tons The tonne ( or ; symbol: t) is a unit of mass equal to 1000  kilograms. It is a non-SI unit accepted for use with SI. It is also referred to as a metric ton to distinguish it from the non-metric units of the short ton ( United State ...
of silicon per year)


Silica cycle

The diagram shows the major
flux Flux describes any effect that appears to pass or travel (whether it actually moves or not) through a surface or substance. Flux is a concept in applied mathematics and vector calculus which has many applications to physics. For transport ...
es of
silicon Silicon is a chemical element with the symbol Si and atomic number 14. It is a hard, brittle crystalline solid with a blue-grey metallic luster, and is a tetravalent metalloid and semiconductor. It is a member of group 14 in the periodic ...
in the current ocean. Most
biogenic silica Biogenic silica (bSi), also referred to as opal, biogenic opal, or amorphous opaline silica, forms one of the most widespread biogenic minerals. For example, microscopic particles of silica called phytoliths can be found in grasses and other plant ...
in the ocean (
silica Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is ...
produced by
biological activity In pharmacology, biological activity or pharmacological activity describes the beneficial or adverse effects of a drug on living matter. When a drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or ...
) comes from diatoms. Diatoms extract dissolved
silicic acid Silicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz and in various living organisms. In many parts of the world, silica is the major constituent of sand. Silica is one ...
from surface waters as they grow, and return it to the
water column A water column is a conceptual column of water from the surface of a sea, river or lake to the bottom sediment.Munson, B.H., Axler, R., Hagley C., Host G., Merrick G., Richards C. (2004).Glossary. ''Water on the Web''. University of Minnesota-D ...
when they die. Inputs of silicon arrive from above via aeolian dust, from the coasts via rivers, and from below via
seafloor sediment Marine sediment, or ocean sediment, or seafloor sediment, are deposits of insoluble particles that have accumulated on the seafloor. These particles have their origins in soil and rocks and have been transported from the land to the sea, main ...
recycling, weathering, and hydrothermal activity. Although diatoms may have existed since the
Triassic The Triassic ( ) is a geologic period and system which spans 50.6 million years from the end of the Permian Period 251.902 million years ago ( Mya), to the beginning of the Jurassic Period 201.36 Mya. The Triassic is the first and shortest per ...
, the timing of their ascendancy and "take-over" of the silicon cycle occurred more recently. Prior to the
Phanerozoic The Phanerozoic Eon is the current geologic eon in the geologic time scale, and the one during which abundant animal and plant life has existed. It covers 538.8 million years to the present, and it began with the Cambrian Period, when anim ...
(before 544 Ma), it is believed that
microbial A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
or
inorganic In chemistry, an inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds, that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as ''inorganic chemist ...
processes weakly regulated the ocean's silicon cycle. Subsequently, the cycle appears dominated (and more strongly regulated) by the
radiolaria The Radiolaria, also called Radiozoa, are protozoa of diameter 0.1–0.2 mm that produce intricate mineral skeletons, typically with a central capsule dividing the cell into the inner and outer portions of endoplasm and ectoplasm. The el ...
ns and siliceous sponges, the former as
zooplankton Zooplankton are the animal component of the planktonic community ("zoo" comes from the Greek word for ''animal''). Plankton are aquatic organisms that are unable to swim effectively against currents, and consequently drift or are carried along by ...
, the latter as sedentary
filter-feeder Filter feeders are a sub-group of suspension feeding animals that feed by straining suspended matter and food particles from water, typically by passing the water over a specialized filtering structure. Some animals that use this method of feedin ...
s primarily on the
continental shelves A continental shelf is a portion of a continent that is submerged under an area of relatively shallow water, known as a shelf sea. Much of these shelves were exposed by drops in sea level during glacial periods. The shelf surrounding an island ...
. Within the last 100 My, it is thought that the silicon cycle has come under even tighter control, and that this derives from the ecological ascendancy of the diatoms. However, the precise timing of the "take-over" remains unclear, and different authors have conflicting interpretations of the fossil record. Some evidence, such as the displacement of siliceous sponges from the shelves, suggests that this takeover began in the Cretaceous (146 Ma to 66 Ma), while evidence from radiolarians suggests "take-over" did not begin until the
Cenozoic The Cenozoic ( ; ) is Earth's current geological era, representing the last 66million years of Earth's history. It is characterised by the dominance of mammals, birds and flowering plants, a cooling and drying climate, and the current configu ...
(66 Ma to present). File:Ocean carbon cycle and diatom carbon dioxide concentration mechanisms 2.jpg, upright=1.8, Ocean carbon cycle and diatom carbon dioxide concentration mechanisms Modified material was copied from this source, which is available under
Creative Commons Attribution 4.0 International License


Carbon cycle

The diagram depicts some mechanisms by which marine diatoms contribute to the biological carbon pump and influence the ocean carbon cycle. The anthropogenic CO2 emission to the atmosphere (mainly generated by fossil fuel burning and deforestation) is nearly 11
gigatonne The tonne ( or ; symbol: t) is a unit of mass equal to 1000 kilograms. It is a non-SI unit accepted for use with SI. It is also referred to as a metric ton to distinguish it from the non-metric units of the short ton (United States c ...
carbon (GtC) per year, of which almost 2.5 GtC is taken up by the surface ocean. In surface seawater ( pH 8.1–8.4),
bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial biochemi ...
() and
carbonate A carbonate is a salt of carbonic acid (H2CO3), characterized by the presence of the carbonate ion, a polyatomic ion with the formula . The word ''carbonate'' may also refer to a carbonate ester, an organic compound containing the carbonate ...
ions () constitute nearly 90 and <10% of dissolved inorganic carbon (DIC) respectively, while dissolved CO2 (CO2 aqueous) contributes <1%. Despite this low level of CO2 in the ocean and its slow
diffusion rate Diffusion is the net movement of anything (for example, atoms, ions, molecules, energy) generally from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in Gibbs free energy or chemical ...
in water, diatoms fix 10–20 GtC annually via photosynthesis thanks to their
carbon dioxide concentrating mechanism Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is converted to organic compounds by living organisms. The compounds are then used to store energy and ...
s, allowing them to sustain
marine food chain Compared to terrestrial environments, marine environments have biomass pyramids which are inverted at the base. In particular, the biomass of consumers (copepods, krill, shrimp, forage fish) is larger than the biomass of primary producers. This ...
s. In addition, 0.1–1% of this organic material produced in the euphotic layer sinks down as particles, thus transferring the surface carbon toward the deep ocean and sequestering atmospheric CO2 for thousands of years or longer. The remaining
organic matter Organic matter, organic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. It is matter composed of organic compounds that have c ...
is remineralized through respiration. Thus, diatoms are one of the main players in this biological carbon pump, which is arguably the most important biological mechanism in the Earth System allowing CO2 to be removed from the
carbon cycle The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Carbon is the main component of biological compounds as well as a major compon ...
for very long period. File:Urea cycle in a diatom.jpg, Mitochondrial urea cycle in a generic diatom cell and the potential fates of urea cycle intermediates Modified material was copied from this source, which is available under
Creative Commons Attribution 4.0 International License


Urea cycle

A feature of diatoms is the
urea cycle The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions that produces urea (NH2)2CO from ammonia (NH3). Animals that use this cycle, mainly amphibians and mammals, are called ureotelic. The urea cycle converts h ...
, which links them evolutionarily to animals. In 2011, Allen et al. established that diatoms have a functioning urea cycle. This result was significant, since prior to this, the urea cycle was thought to have originated with the metazoans which appeared several hundreds of millions of years before the diatoms. Their study demonstrated that while diatoms and animals use the urea cycle for different ends, they are seen to be evolutionarily linked in such a way that animals and plants are not. While often overlooked in photosynthetic organisms, the
mitochondria A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
also play critical roles in energy balance. Two nitrogen-related pathways are relevant and they may also change under
ammonium The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaterna ...
() nutrition compared with
nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an insolu ...
() nutrition. First, in diatoms, and likely some other algae, there is a urea cycle. The long-known function of the urea cycle in animals is to excrete excess nitrogen produced by amino acid catabolism; like
photorespiration Photorespiration (also known as the oxidative photosynthetic carbon cycle or C2 cycle) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. The desired reactio ...
, the urea cycle had long been considered a waste pathway. However, in diatoms the urea cycle appears to play a role in exchange of nutrients between the mitochondria and the
cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. ...
, and potentially the
plastid The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cyan ...
and may help to regulate ammonium metabolism. Because of this cycle, marine diatoms, in contrast to
chlorophyte Chlorophyta or Prasinophyta is a taxon of green algae informally called chlorophytes. The name is used in two very different senses, so care is needed to determine the use by a particular author. In older classification systems, it refers to a ...
s, also have acquired a mitochondrial
urea transporter A urea transporter is a membrane transport protein, transporting urea. Humans and other mammals have two types of urea transport proteins, UT-A and UT-B. The UT-A proteins are important for renal urea handling and are produced by alternative sp ...
and, in fact, based on
bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
, a complete mitochondrial GS-GOGAT cycle has been hypothesised.


Other

Diatoms are mainly photosynthetic; however a few are obligate heterotrophs and can live in the absence of light provided an appropriate organic carbon source is available. Photosynthetic diatoms that find themselves in an environment absent of oxygen and/or sunlight can switch to anaerobic respiration known as nitrate respiration (DNRA), and stay dormant for up till months and decades. Major
pigment A pigment is a colored material that is completely or nearly insoluble in water. In contrast, dyes are typically soluble, at least at some stage in their use. Generally dyes are often organic compounds whereas pigments are often inorganic compou ...
s of diatoms are
chlorophylls Chlorophyll (also chlorophyl) is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words , ("pale green") and , ("leaf"). Chlorophyll allow plants to ...
a and c, beta-carotene, fucoxanthin, diatoxanthin and diadinoxanthin.


Taxonomy

Diatoms belong to a large group of protists, many of which contain plastids rich in chlorophylls a and c. The group has been variously referred to as
heterokont Heterokonts are a group of protists (formally referred to as Heterokonta, Heterokontae or Heterokontophyta). The group is a major line of eukaryotes. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms, which a ...
s, chrysophytes,
chromist Chromista is a biological kingdom consisting of single-celled and multicellular eukaryotic species that share similar features in their photosynthetic organelles ( plastids). It includes all protists whose plastids contain chlorophyll ''c'', ...
s or
stramenopile Stramenopile is a clade of organisms distinguished by the presence of stiff tripartite external hairs. In most species, the hairs are attached to flagella, in some they are attached to other areas of the cellular surface, and in some they have be ...
s. Many are
autotroph An autotroph or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide,Morris, J. et al. (2019). "Biology: How Life Wo ...
s such as golden algae and
kelp Kelps are large brown algae seaweeds that make up the order Laminariales. There are about 30 different genera. Despite its appearance, kelp is not a plant - it is a heterokont, a completely unrelated group of organisms. Kelp grows in "underwa ...
; and
heterotroph A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...
s such as
water mould Oomycota forms a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, called oomycetes (). They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the r ...
s, opalinids, and actinophryid heliozoa. The classification of this area of protists is still unsettled. In terms of rank, they have been treated as a
division Division or divider may refer to: Mathematics *Division (mathematics), the inverse of multiplication *Division algorithm, a method for computing the result of mathematical division Military *Division (military), a formation typically consisting ...
,
phylum In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature ...
, kingdom, or something intermediate to those. Consequently, diatoms are ranked anywhere from a class, usually called Diatomophyceae or Bacillariophyceae, to a division (=phylum), usually called Bacillariophyta, with corresponding changes in the ranks of their subgroups.


Genera and species

An estimated 20,000
extant Extant is the opposite of the word extinct. It may refer to: * Extant hereditary titles * Extant literature, surviving literature, such as ''Beowulf'', the oldest extant manuscript written in English * Extant taxon, a taxon which is not extinct, ...
diatom
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriat ...
are believed to exist, of which around 12,000 have been named to date according to Guiry, 2012 (other sources give a wider range of estimatesCanter-Lund, H. and Lund, J.W.G. (1995). ''Freshwater Algae: Their microscopic world explained'', Biopress Limited. .). Around 1,000–1,300 diatom genera have been described, both extant and fossil, of which some 250–300 exist only as fossils.


Classes and orders

For many years the diatoms—treated either as a class (Bacillariophyceae) or a phylum (Bacillariophyta)—were divided into just 2 orders, corresponding to the centric and the pennate diatoms (
Centrales The Coscinodiscophyceae are a class of diatoms. They are similar to the Centrales, a traditional, paraphyletic subdivision of the heterokont algae known as diatoms. The order is named for the shape of the cell walls (or valves or frustules) of ...
and
Pennales The order Pennales is a traditional subdivision of the heterokont algae known as diatoms. The order is named for the shape of the cell walls (or valves or frustules) of pennate diatoms, which are elongated in valve view. The valves may be linear ...
). This classification was extensively overhauled by Round, Crawford and Mann in 1990 who treated the diatoms at a higher rank (division, corresponding to phylum in zoological classification), and promoted the major classification units to classes, maintaining the centric diatoms as a single class Coscinodiscophyceae, but splitting the former pennate diatoms into 2 separate classes,
Fragilariophyceae Fragilariophyceae is a group of pennate diatoms lacking a raphe. Examples It includes the following genera: Fragilariales *'' Ardissonea'' *'' Asterionella'' *'' Asterionellopsis'' *'' Catacombas'' *'' Diatoma'' *'' Fragilaria'' *'' Fragilarif ...
and Bacillariophyceae (the latter older name retained but with an emended definition), between them encompassing 45 orders, the majority of them new. Today (writing at mid 2020) it is recognised that the 1990 system of Round et al. is in need of revision with the advent of newer molecular work, however the best system to replace it is unclear, and current systems in widespread use such as
AlgaeBase AlgaeBase is a global species database of information on all groups of algae, both marine and freshwater, as well as sea-grass. History AlgaeBase began in March 1996, founded by Michael Guiry. Text was copied from this source, which is avail ...
, the World Register of Marine Species and its contributing database DiatomBase, and the system for "all life" represented in Ruggiero et al., 2015, all retain the Round et al. treatment as their basis, albeit with diatoms as a whole treated as a class rather than division/phylum, and Round et al.'s classes reduced to subclasses, for better agreement with the treatment of phylogenetically adjacent groups and their containing taxa. (For references refer the individual sections below). One proposal, by Linda Medlin and co-workers commencing in 2004, is for some of the centric diatom orders considered more closely related to the pennates to be split off as a new class, Mediophyceae, itself more closely aligned with the pennate diatoms than the remaining centrics. This hypothesis—later designated the Coscinodiscophyceae-Mediophyceae-Bacillariophyceae, or Coscinodiscophyceae+(Mediophyceae+Bacillariophyceae) (CMB) hypothesis—has been accepted by D.G. Mann among others, who uses it as the basis for the classification of diatoms as presented in Adl. et al.'s series of syntheses (2005, 2012, 2019), and also in the Bacillariophyta chapter of the 2017 ''Handbook of the Protists'' edited by Archibald et al., with some modifications reflecting the apparent non-monophyly of Medlin et al. original "Coscinodiscophyceae". Meanwhile, a group led by E.C. Theriot favours a different hypothesis of phylogeny, which has been termed the structural gradation hypothesis (SGH) and does not recognise the Mediophyceae as a monophyletic group, while another analysis, that of Parks et al., 2018, finds that the radial centric diatoms (Medlin et al.'s Coscinodiscophyceae) are not monophyletic, but supports the monophyly of Mediophyceae minus ''
Attheya ''Attheya'' is a genus of small single celled diatoms. Some of these species were earlier regarded to belong to '' Chaetoceros'', or to '' Gonioceros'', the taxonomic status of some of these species are still debated.Crawford, R.M., Hinz, F. and ...
'', which is an anomalous genus. Discussion of the relative merits of these conflicting schemes continues by the various parties involved.


Adl et al., 2019 treatment

In 2019, Adl ''et al.'' presented the following classification of diatoms, while noting: "This revision reflects numerous advances in the phylogeny of the diatoms over the last decade. Due to our poor taxon sampling outside of the Mediophyceae and pennate diatoms, and the known and anticipated diversity of all diatoms, many clades appear at a high classification level (and the higher level classification is rather flat)." This classification treats diatoms as a phylum (Diatomeae/Bacillariophyta), accepts the class Mediophyceae of Medlin and co-workers, introduces new subphyla and classes for a number of otherwise isolated genera, and re-ranks a number of previously established taxa as subclasses, but does not list orders or families. Inferred ranks have been added for clarity (Adl. et al. do not use ranks, but the intended ones in this portion of the classification are apparent from the choice of endings used, within the system of botanical nomenclature employed). * Clade Diatomista Derelle et al. 2016, emend. Cavalier-Smith 2017 (diatoms plus a subset of other ochrophyte groups) :* Phylum Diatomeae Dumortier 1821 _Bacillariophyta_Haeckel_1878.html" ;"title="Bacillariophyta.html" ;"title=" Bacillariophyta"> Bacillariophyta Haeckel 1878">Bacillariophyta.html" ;"title=" Bacillariophyta"> Bacillariophyta Haeckel 1878(diatoms) ::* Subphylum Leptocylindrophytina D.G. Mann in Adl et al. 2019 :::* Class Leptocylindrophyceae D.G. Mann in Adl et al. 2019 (''Leptocylindrus'', ''Tenuicylindrus'') :::* Class Corethrophyceae D.G. Mann in Adl et al. 2019 (''Corethron'') ::* Subphylum Ellerbeckiophytina D.G. Mann in Adl et al. 2019 (''
Ellerbeckia ''Ellerbeckia'' is a genus of diatom A diatom ( Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is a ...
'') ::* Subphylum Probosciophytina D.G. Mann in Adl et al. 2019 ('' Proboscia'') ::* Subphylum Melosirophytina D.G. Mann in Adl et al. 2019 (''
Aulacoseira ''Aulacoseira'' is a genus of diatoms belonging to the family Aulacoseiraceae. The genus has cosmopolitan distribution In biogeography, cosmopolitan distribution is the term for the range of a taxon that extends across all or most of the w ...
'', ''
Melosira ''Melosira'' is a genus of diatoms belonging to the family Melosiraceae. The genus has cosmopolitan distribution In biogeography, cosmopolitan distribution is the term for the range of a taxon that extends across all or most of the world i ...
'', ''
Hyalodiscus ''Hyalodiscus'' is an extant genus of diatom known also from the fossil A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, she ...
'', '' Stephanopyxis'', '' Paralia'', '' Endictya'') ::* Subphylum Coscinodiscophytina Medlin & Kaczmarska 2004, emend. (''
Actinoptychus ''Actinoptychus'' is a genus of diatoms belonging to the family Heliopeltaceae. The genus was described in 1843 by Christian Gottfried Ehrenberg Christian Gottfried Ehrenberg (19 April 1795 – 27 June 1876) was a German naturalist, zoologi ...
'', ''
Coscinodiscus ''Coscinodiscus'' is a genus of diatoms in the family Coscinodiscaceae. It is the type genus of its family. References External links * * ''Coscinodiscus'' at the World Register of Marine Species (WoRMS) {{Taxonbar, from=Q12744 ...
'', ''
Actinocyclus ''Actinocyclus'' is a genus of sea slugs, dorid nudibranchs, shell-less marine gastropod molluscs in the family Actinocyclidae,Rosenberg, G. (2012). ''Actinocyclus'' Ehrenberg, 1831. Accessed through: World Register of Marine Species at ht ...
'', '' Asteromphalus'', '' Aulacodiscus'', '' Stellarima'') ::* Subphylum Rhizosoleniophytina D.G. Mann in Adl et al. 2019 (''
Guinardia ''Guinardia'' is a genus of diatoms belonging to the family Rhizosoleniaceae. The genus was first described by H. Peragallo in 1892. The genus has cosmopolitan distribution In biogeography, cosmopolitan distribution is the term for the r ...
'', '' Rhizosolenia'', '' Pseudosolenia'') ::* Subphylum Arachnoidiscophytina D.G. Mann in Adl et al. 2019 ('' Arachnoidiscus'') ::* Subphylum Bacillariophytina Medlin & Kaczmarska 2004, emend. :::* Class Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004 ::::* Subclass Chaetocerotophycidae Round & R.M. Crawford in Round et al. 1990, emend. ::::* Subclass Lithodesmiophycidae Round & R.M. Crawford in Round et al. 1990, emend. ::::* Subclass Thalassiosirophycidae Round & R.M. Crawford in Round et al. 1990 ::::* Subclass Cymatosirophycidae Round & R.M. Crawford in Round et al. 1990 ::::* Subclass Odontellophycidae D.G. Mann in Adl et al. 2019 ::::* Subclass Chrysanthemodiscophycidae D.G. Mann in Adl et al. 2019 :::* Class Biddulphiophyceae D.G. Mann in Adl et al. 2019 ::::* Subclass Biddulphiophycidae Round and R.M. Crawford in Round et al. 1990, emend. ::::* Biddulphiophyceae incertae sedis (''
Attheya ''Attheya'' is a genus of small single celled diatoms. Some of these species were earlier regarded to belong to '' Chaetoceros'', or to '' Gonioceros'', the taxonomic status of some of these species are still debated.Crawford, R.M., Hinz, F. and ...
'') :::* Class
Bacillariophyceae Bacillariophyceae is a group of pennate diatoms with a raphe (raphids). According to Ruggiero et al., 2015, the diatoms are treated as follows. This treatment largely reflects that used by Algaebase as at 2015, and is also reflected in the current ...
Haeckel 1878, emend. ::::* Bacillariophyceae incertae sedis (Striatellaceae) ::::* Subclass Urneidophycidae Medlin 2016 ::::* Subclass Fragilariophycidae Round in Round, Crawford & Mann 1990, emend. ::::* Subclass Bacillariophycidae D.G. Mann in Round, Crawford & Mann 1990, emend. See
taxonomy of diatoms Diatoms belong to a large group called the heterokonts, which include both autotrophs such as golden algae and kelp; and heterotrophs such as water moulds. The classification of heterokonts is still unsettled: they may be designated a Division (bo ...
for more details.


Gallery

File:Surirella spiralis - SEM MUSE - sharpened.jpeg, Diatom ''Surirella spiralis'' File:Diatoms-HCMR.jpg, Diatoms ''Thalassiosira'' sp. on a membrane filter, pore size 0.4 μm. File:Paralia sulcata diatom.tif, Diatom ''Paralia sulcata''. File:Achanthes trinodis - SEM MUSE.tiff, Diatom ''Achanthes trinodis'' File:Bacillaria paxillifera.jpg, Stand-alone cell of ''
Bacillaria paxillifer ''Bacillaria paxillifer'' is a colonial diatom A diatom ( Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twa ...
'' File:Bacillaria paxillifer.tif, Colonial group of ''Bacillaria paxillifer''
Three diatom species were sent to the
International Space Station The International Space Station (ISS) is the largest Modular design, modular space station currently in low Earth orbit. It is a multinational collaborative project involving five participating space agencies: NASA (United States), Roscosmos ( ...
, including the huge (6 mm length) diatoms of Antarctica and the exclusive colonial diatom, ''Bacillaria paradoxa''. The cells of ''Bacillaria'' moved next to each other in partial but opposite synchrony by a microfluidics method.


Evolution and fossil record


Origin

Heterokont chloroplasts appear to derive from those of
red algae Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
, rather than directly from
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
s as occurred in
plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae excl ...
s. This suggests they had a more recent origin than many other algae. However, fossil evidence is scant, and only with the evolution of the diatoms themselves do the heterokonts make a serious impression on the fossil record.


Earliest fossils

The earliest known fossil diatoms date from the early
Jurassic The Jurassic ( ) is a geologic period and stratigraphic system that spanned from the end of the Triassic Period million years ago (Mya) to the beginning of the Cretaceous Period, approximately Mya. The Jurassic constitutes the middle period of ...
(~185 Ma ago), although the
molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleo ...
and
sedimentary Sedimentary rocks are types of rock that are formed by the accumulation or deposition of mineral or organic particles at Earth's surface, followed by cementation. Sedimentation is the collective name for processes that cause these particles ...
evidence suggests an earlier origin. It has been suggested that their origin may be related to the end-Permian mass extinction (~250 Ma), after which many marine niches were opened. The gap between this event and the time that fossil diatoms first appear may indicate a period when diatoms were unsilicified and their evolution was
cryptic Cryptic may refer to: In science: * Cryptic species complex, a group of species that are very difficult to distinguish from one another * Crypsis, the ability of animals to blend in to avoid observation * Cryptic era, earliest period of the Earth ...
. Since the advent of silicification, diatoms have made a significant impression on the fossil record, with major fossil deposits found as far back as the early
Cretaceous The Cretaceous ( ) is a geological period that lasted from about 145 to 66 million years ago (Mya). It is the third and final period of the Mesozoic Era, as well as the longest. At around 79 million years, it is the longest geological period of ...
, and with some rocks such as
diatomaceous earth Diatomaceous earth (), diatomite (), or kieselgur/kieselguhr is a naturally occurring, soft, siliceous sedimentary rock that can be crumbled into a fine white to off-white powder. It has a particle size ranging from more than 3 μm to l ...
, being composed almost entirely of them.


Relation to grasslands

The expansion of
grassland A grassland is an area where the vegetation is dominated by grasses ( Poaceae). However, sedge ( Cyperaceae) and rush ( Juncaceae) can also be found along with variable proportions of legumes, like clover, and other herbs. Grasslands occur na ...
biome A biome () is a biogeographical unit consisting of a biological community that has formed in response to the physical environment in which they are found and a shared regional climate. Biomes may span more than one continent. Biome is a broader ...
s and the
evolutionary radiation An evolutionary radiation is an increase in taxonomic diversity that is caused by elevated rates of speciation, that may or may not be associated with an increase in morphological disparity. Radiations may affect one clade or many, and be rapid ...
of
grass Poaceae () or Gramineae () is a large and nearly ubiquitous family of monocotyledonous flowering plants commonly known as grasses. It includes the cereal grasses, bamboos and the grasses of natural grassland and species cultivated in lawns a ...
es during the
Miocene The Miocene ( ) is the first geological epoch of the Neogene Period and extends from about (Ma). The Miocene was named by Scottish geologist Charles Lyell; the name comes from the Greek words (', "less") and (', "new") and means "less recen ...
is believed to have increased the flux of soluble silicon to the oceans, and it has been argued that this promoted the diatoms during the Cenozoic era. Recent work suggests that diatom success is decoupled from the evolution of grasses, although both diatom and grassland diversity increased strongly from the middle Miocene.


Relation to climate

Diatom diversity over the Cenozoic has been very sensitive to global temperature, particularly to the equator-pole temperature gradient. Warmer oceans, particularly warmer polar regions, have in the past been shown to have had substantially lower diatom diversity. Future warm oceans with enhanced polar warming, as projected in global-warming scenarios, could thus in theory result in a significant loss of diatom diversity, although from current knowledge it is impossible to say if this would occur rapidly or only over many tens of thousands of years.


Method of investigation

The fossil record of diatoms has largely been established through the recovery of their siliceous
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
s in marine and non-marine sediments. Although diatoms have both a marine and non-marine stratigraphic record, diatom
biostratigraphy Biostratigraphy is the branch of stratigraphy which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages contained within them.Hine, Robert. “Biostratigraphy.” ''Oxford Reference: Dictionary of ...
, which is based on time-constrained evolutionary originations and extinctions of unique taxa, is only well developed and widely applicable in marine systems. The duration of diatom species ranges have been documented through the study of ocean cores and rock sequences exposed on land. Where diatom
biozone In biostratigraphy, biostratigraphic units or biozones are intervals of geological strata that are defined on the basis of their characteristic fossil taxa, as opposed to a lithostratigraphic unit which is defined by the lithological properties ...
s are well established and calibrated to the geomagnetic polarity time scale (e.g.,
Southern Ocean The Southern Ocean, also known as the Antarctic Ocean, comprises the southernmost waters of the World Ocean, generally taken to be south of 60° S latitude and encircling Antarctica. With a size of , it is regarded as the second-smal ...
,
North Pacific The Pacific Ocean is the largest and deepest of Earth's five oceanic divisions. It extends from the Arctic Ocean in the north to the Southern Ocean (or, depending on definition, to Antarctica) in the south, and is bounded by the continen ...
, eastern equatorial
Pacific The Pacific Ocean is the largest and deepest of Earth's five oceanic divisions. It extends from the Arctic Ocean in the north to the Southern Ocean (or, depending on definition, to Antarctica) in the south, and is bounded by the contine ...
), diatom-based age estimates may be resolved to within <100,000 years, although typical age resolution for
Cenozoic The Cenozoic ( ; ) is Earth's current geological era, representing the last 66million years of Earth's history. It is characterised by the dominance of mammals, birds and flowering plants, a cooling and drying climate, and the current configu ...
diatom assemblages is several hundred thousand years. Diatoms preserved in lake sediments are widely used for paleoenvironmental reconstructions of
Quaternary The Quaternary ( ) is the current and most recent of the three periods of the Cenozoic Era in the geologic time scale of the International Commission on Stratigraphy (ICS). It follows the Neogene Period and spans from 2.58 million year ...
climate, especially for closed-basin lakes which experience fluctuations in water depth and salinity.


Isotope records

When diatoms die their shells (
frustule A frustule is the hard and porous cell wall or external layer of diatoms. The frustule is composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, which was referred to in the early literature on ...
s) can settle on the
seafloor The seabed (also known as the seafloor, sea floor, ocean floor, and ocean bottom) is the bottom of the ocean The ocean (also the sea or the world ocean) is the body of salt water that covers approximately 70.8% of the surface of Earth an ...
and become
microfossil A microfossil is a fossil that is generally between 0.001 mm and 1 mm in size, the visual study of which requires the use of light or electron microscopy. A fossil which can be studied with the naked eye or low-powered magnification, ...
s. Over time, these microfossils become buried as
opal Opal is a hydrated amorphous form of silica (SiO2·''n''H2O); its water content may range from 3 to 21% by weight, but is usually between 6 and 10%. Due to its amorphous property, it is classified as a mineraloid, unlike crystalline form ...
deposits in the
marine sediment Marine sediment, or ocean sediment, or seafloor sediment, are deposits of insoluble particles that have accumulated on the seafloor. These particles have their origins in soil and rocks and have been transported from the land to the sea, mai ...
.
Paleoclimatology Paleoclimatology (British spelling, palaeoclimatology) is the study of climates for which direct measurements were not taken. As instrumental records only span a tiny part of Earth's history, the reconstruction of ancient climate is important to ...
is the study of past climates. Proxy data is used in order to relate elements collected in modern-day sedimentary samples to climatic and oceanic conditions in the past.
Paleoclimate proxies Paleolimnology (from Greek: παλαιός, ''palaios'', "ancient", λίμνη, ''limne'', "lake", and λόγος, ''logos'', "study") is a scientific sub-discipline closely related to both limnology and paleoecology. Paleolimnological studies ...
refer to preserved or fossilized physical markers which serve as substitutes for direct meteorological or ocean measurements. An example of proxies is the use of diatom isotope records of
δ13C In geochemistry, paleoclimatology, and paleoceanography ''δ''13C (pronounced "delta c thirteen") is an isotopic signature, a measure of the ratio of stable isotopes 13C : 12C, reported in parts per thousand (per mil, ‰). The measure is al ...
, δ18O, δ30Si (δ13Cdiatom, δ18Odiatom, and δ30Sidiatom). In 2015, Swann and Snelling used these isotope records to document historic changes in the photic zone conditions of the north-west
Pacific Ocean The Pacific Ocean is the largest and deepest of Earth's five oceanic divisions. It extends from the Arctic Ocean in the north to the Southern Ocean (or, depending on definition, to Antarctica) in the south, and is bounded by the conti ...
, including nutrient supply and the efficiency of the soft-tissue
biological pump The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments.Sigman DM & GH ...
, from the modern day back to
marine isotope stage 5e Marine Isotope Stage 5 or MIS 5 is a marine isotope stage in the geologic temperature record, between 130,000 and 80,000 years ago. Sub-stage MIS 5e, called the Eemian or Ipswichian, covers the last major interglacial period before the Holocene, w ...
, which coincides with the last interglacial period. Peaks in opal productivity in the marine isotope stage are associated with the breakdown of the regional halocline stratification and increased nutrient supply to the
photic zone The photic zone, euphotic zone, epipelagic zone, or sunlight zone is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological pro ...
. Material was copied from this source, which is available under
Creative Commons Attribution 3.0 International License
.
File:Ocean changes from the last interglacial to the modern day A.png File:Ocean changes from the last interglacial to the modern day B.png The initial development of the halocline and stratified water column has been attributed to the onset of major Northern Hemisphere glaciation at 2.73 Ma, which increased the flux of freshwater to the region, via increased monsoonal rainfall and/or glacial meltwater, and sea surface temperatures. The decrease of abyssal water upwelling associated with this may have contributed to the establishment of globally cooler conditions and the expansion of glaciers across the Northern Hemisphere from 2.73 Ma. While the halocline appears to have prevailed through the
late Pliocene Late may refer to: * LATE, an acronym which could stand for: ** Limbic-predominant age-related TDP-43 encephalopathy, a proposed form of dementia ** Local-authority trading enterprise, a New Zealand business law ** Local average treatment effe ...
and early Quaternary glacial–interglacial cycles, other studies have shown that the stratification boundary may have broken down in the late Quaternary at glacial terminations and during the early part of interglacials.


Diversification

The
Cretaceous The Cretaceous ( ) is a geological period that lasted from about 145 to 66 million years ago (Mya). It is the third and final period of the Mesozoic Era, as well as the longest. At around 79 million years, it is the longest geological period of ...
record of diatoms is limited, but recent studies reveal a progressive diversification of diatom types. The
Cretaceous–Paleogene extinction event The Cretaceous–Paleogene (K–Pg) extinction event (also known as the Cretaceous–Tertiary extinction) was a sudden mass extinction of three-quarters of the plant and animal species on Earth, approximately 66 million years ago. With the ...
, which in the oceans dramatically affected organisms with calcareous skeletons, appears to have had relatively little impact on diatom evolution.


Turnover

Although no mass extinctions of marine diatoms have been observed during the
Cenozoic The Cenozoic ( ; ) is Earth's current geological era, representing the last 66million years of Earth's history. It is characterised by the dominance of mammals, birds and flowering plants, a cooling and drying climate, and the current configu ...
, times of relatively rapid evolutionary turnover in marine diatom species assemblages occurred near the
Paleocene The Paleocene, ( ) or Palaeocene, is a geological epoch that lasted from about 66 to 56 million years ago (mya). It is the first epoch of the Paleogene Period in the modern Cenozoic Era. The name is a combination of the Ancient Greek ''pala ...
Eocene The Eocene ( ) Epoch is a geological epoch that lasted from about 56 to 33.9 million years ago (mya). It is the second epoch of the Paleogene Period in the modern Cenozoic Era. The name ''Eocene'' comes from the Ancient Greek (''ēṓs'', ...
boundary, and at the
Eocene The Eocene ( ) Epoch is a geological epoch that lasted from about 56 to 33.9 million years ago (mya). It is the second epoch of the Paleogene Period in the modern Cenozoic Era. The name ''Eocene'' comes from the Ancient Greek (''ēṓs'', ...
Oligocene The Oligocene ( ) is a geologic epoch of the Paleogene Period and extends from about 33.9 million to 23 million years before the present ( to ). As with other older geologic periods, the rock beds that define the epoch are well identified but t ...
boundary. Further turnover of assemblages took place at various times between the middle
Miocene The Miocene ( ) is the first geological epoch of the Neogene Period and extends from about (Ma). The Miocene was named by Scottish geologist Charles Lyell; the name comes from the Greek words (', "less") and (', "new") and means "less recen ...
and late
Pliocene The Pliocene ( ; also Pleiocene) is the epoch in the geologic time scale that extends from 5.333 million to 2.58 in response to progressive cooling of polar regions and the development of more endemic diatom assemblages. A global trend toward more delicate diatom frustules has been noted from the
Oligocene The Oligocene ( ) is a geologic epoch of the Paleogene Period and extends from about 33.9 million to 23 million years before the present ( to ). As with other older geologic periods, the rock beds that define the epoch are well identified but t ...
to the
Quaternary The Quaternary ( ) is the current and most recent of the three periods of the Cenozoic Era in the geologic time scale of the International Commission on Stratigraphy (ICS). It follows the Neogene Period and spans from 2.58 million year ...
. This coincides with an increasingly more vigorous circulation of the ocean's surface and deep waters brought about by increasing latitudinal thermal gradients at the onset of major
ice sheet In glaciology, an ice sheet, also known as a continental glacier, is a mass of glacial ice that covers surrounding terrain and is greater than . The only current ice sheets are in Antarctica and Greenland; during the Last Glacial Period at La ...
expansion on
Antarctica Antarctica () is Earth's southernmost and least-populated continent. Situated almost entirely south of the Antarctic Circle and surrounded by the Southern Ocean, it contains the geographic South Pole. Antarctica is the fifth-largest cont ...
and progressive cooling through the
Neogene The Neogene ( ), informally Upper Tertiary or Late Tertiary, is a geologic period and system that spans 20.45 million years from the end of the Paleogene Period million years ago ( Mya) to the beginning of the present Quaternary Period Mya. ...
and
Quaternary The Quaternary ( ) is the current and most recent of the three periods of the Cenozoic Era in the geologic time scale of the International Commission on Stratigraphy (ICS). It follows the Neogene Period and spans from 2.58 million year ...
towards a bipolar glaciated world. This caused diatoms to take in less silica for the formation of their frustules. Increased mixing of the oceans renews silica and other nutrients necessary for diatom growth in surface waters, especially in regions of coastal and oceanic
upwelling Upwelling is an physical oceanography, oceanographic phenomenon that involves wind-driven motion of dense, cooler, and usually nutrient-rich water from deep water towards the ocean surface. It replaces the warmer and usually nutrient-depleted ...
.


Genetics


Expressed sequence tagging

In 2002, the first insights into the properties of the ''
Phaeodactylum tricornutum ''Phaeodactylum tricornutum'' is a diatom. It is the only species in the genus ''Phaeodactylum''. Unlike other diatoms, ''P. tricornutum'' can exist in different morphotypes (fusiform, triradiate, and oval) and changes in cell shape can be stimul ...
'' gene repertoire were described using 1,000
expressed sequence tag In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proc ...
s (ESTs). Subsequently, the number of ESTs was extended to 12,000 and the diatom EST database was constructed for functional analyses. These sequences have been used to make a comparative analysis between ''P. tricornutum'' and the putative complete proteomes from the
green alga The green algae (singular: green alga) are a group consisting of the Prasinodermophyta and its unnamed sister which contains the Chlorophyta and Charophyta/Streptophyta. The land plants (Embryophytes) have emerged deep in the Charophyte alga as ...
''
Chlamydomonas reinhardtii ''Chlamydomonas reinhardtii'' is a single-cell green alga about 10 micrometres in diameter that swims with two flagella. It has a cell wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid, and an eye ...
'', the
red alga Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
''
Cyanidioschyzon merolae ''Cyanidioschyzon merolae'' is a small (2μm), club-shaped, unicellular haploid red alga adapted to high sulfur acidic hot spring environments (pH 1.5, 45 °C). The cellular architecture of ''C. merolae'' is extremely simple, containing only ...
'', and the diatom '' Thalassiosira pseudonana''. The diatom EST database now consists of over 200,000 ESTs from ''P. tricornutum'' (16 libraries) and ''T. pseudonana'' (7 libraries) cells grown in a range of different conditions, many of which correspond to different abiotic stresses.


Genome sequencing

In 2004, the entire
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
of the centric diatom, '' Thalassiosira pseudonana'' (32.4 Mb) was sequenced, followed in 2008 with the sequencing of the pennate diatom, ''
Phaeodactylum tricornutum ''Phaeodactylum tricornutum'' is a diatom. It is the only species in the genus ''Phaeodactylum''. Unlike other diatoms, ''P. tricornutum'' can exist in different morphotypes (fusiform, triradiate, and oval) and changes in cell shape can be stimul ...
'' (27.4 Mb). Comparisons of the two reveal that the ''P. tricornutum'' genome includes fewer genes (10,402 opposed to 11,776) than ''T. pseudonana''; no major synteny (gene order) could be detected between the two genomes. ''T. pseudonana'' genes show an average of ~1.52 introns per gene as opposed to 0.79 in ''P. tricornutum'', suggesting recent widespread intron gain in the centric diatom. Despite relatively recent evolutionary divergence (90 million years), the extent of molecular divergence between centrics and pennates indicates rapid evolutionary rates within the
Bacillariophyceae Bacillariophyceae is a group of pennate diatoms with a raphe (raphids). According to Ruggiero et al., 2015, the diatoms are treated as follows. This treatment largely reflects that used by Algaebase as at 2015, and is also reflected in the current ...
compared to other
eukaryotic Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
groups.
Comparative genomics Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural ...
also established that a specific class of
transposable elements A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Trans ...
, the Diatom Copia-like retrotransposons (or CoDis), has been significantly amplified in the ''P. tricornutum'' genome with respect to ''T. pseudonana'', constituting 5.8 and 1% of the respective genomes.


Endosymbiotic gene transfer

Diatom genomics brought much information about the extent and dynamics of the endosymbiotic
gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HG ...
(EGT) process. Comparison of the ''T. pseudonana'' proteins with homologs in other organisms suggested that hundreds have their closest homologs in the Plantae lineage. EGT towards diatom genomes can be illustrated by the fact that the ''T. pseudonana'' genome encodes six proteins which are most closely related to genes encoded by the '' Guillardia theta'' (
cryptomonad The cryptomonads (or cryptophytes) are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anteri ...
) nucleomorph genome. Four of these genes are also found in red algal plastid genomes, thus demonstrating successive EGT from red algal plastid to red algal nucleus (nucleomorph) to heterokont host nucleus. More recent phylogenomic analyses of diatom proteomes provided evidence for a
prasinophyte The prasinophytes are a group of unicellular green algae. Prasinophytes mainly include marine planktonic species, as well as some freshwater representatives.Sym, S. D. and Pienaar, R. N. 1993. The class Prasinophyceae. In Round, F. E. and Chapm ...
-like endosymbiont in the common ancestor of
chromalveolates Chromista is a biological kingdom consisting of single-celled and multicellular eukaryotic species that share similar features in their photosynthetic organelles (plastids). It includes all protists whose plastids contain chlorophyll ''c'', such ...
as supported by the fact the 70% of diatom genes of Plantae origin are of green lineage provenance and that such genes are also found in the genome of other
stramenopile Stramenopile is a clade of organisms distinguished by the presence of stiff tripartite external hairs. In most species, the hairs are attached to flagella, in some they are attached to other areas of the cellular surface, and in some they have be ...
s. Therefore, it was proposed that chromalveolates are the product of serial secondary
endosymbiosis An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
first with a
green algae The green algae (singular: green alga) are a group consisting of the Prasinodermophyta and its unnamed sister which contains the Chlorophyta and Charophyta/ Streptophyta. The land plants (Embryophytes) have emerged deep in the Charophyte alga ...
, followed by a second one with a
red algae Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
that conserved the genomic footprints of the previous but displaced the green plastid. However, phylogenomic analyses of diatom proteomes and chromalveolate evolutionary history will likely take advantage of complementary genomic data from under-sequenced lineages such as red algae.


Horizontal gene transfer

In addition to EGT,
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
(HGT) can occur independently of an endosymbiotic event. The publication of the ''P. tricornutum'' genome reported that at least 587 ''P. tricornutum'' genes appear to be most closely related to bacterial genes, accounting for more than 5% of the ''P. tricornutum'' proteome. About half of these are also found in the ''T. pseudonana'' genome, attesting their ancient incorporation in the diatom lineage.


Genetic engineering

To understand the biological mechanisms which underlie the great importance of diatoms in geochemical cycles, scientists have used the ''
Phaeodactylum tricornutum ''Phaeodactylum tricornutum'' is a diatom. It is the only species in the genus ''Phaeodactylum''. Unlike other diatoms, ''P. tricornutum'' can exist in different morphotypes (fusiform, triradiate, and oval) and changes in cell shape can be stimul ...
'' and ''
Thalassiosira ''Thalassiosira'' is a genus of centric diatoms, comprising over 100 marine and freshwater species. It is a diverse group of photosynthetic eukaryotes that make up a vital part of marine and freshwater ecosystems, in which they are key primary pr ...
spp.'' species as model organisms since the 90's. Few molecular biology tools are currently available to generate mutants or transgenic lines :
plasmids A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
containing transgenes are inserted into the cells using the
biolistic In genetic engineering, a gene gun or biolistic particle delivery system is a device used to deliver exogenous DNA (transgenes), RNA, or protein to cells. By coating particles of a heavy metal with a gene of interest and firing these micro-proje ...
method or transkingdom
bacterial conjugation Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in bacter ...
(with 10−6 and 10−4 yield respectively), and other classical transfection methods such as
electroporation Electroporation, or electropermeabilization, is a microbiology technique in which an electrical field is applied to cells in order to increase the permeability of the cell membrane, allowing chemicals, drugs, electrode arrays or DNA to be introd ...
or use of PEG have been reported to provide results with lower efficiencies. Transfected plasmids can be either randomly integrated into the diatom's chromosomes or maintained as stable circular
episomes An episome is a special type of plasmid, which remains as a part of the eukaryotic genome without integration. Episomes manage this by replicating together with the rest of the genome and subsequently associating with metaphase chromosomes during ...
(thanks to the CEN6-ARSH4-HIS3 yeast centromeric sequence). The phleomycin/ zeocin resistance gene Sh Ble is commonly used as a selection marker, and various transgenes have been successfully introduced and expressed in diatoms with stable transmissions through generations, or with the possibility to remove it. Furthermore, these systems now allow the use of the CRISPR-Cas genome edition tool, leading to a fast production of functional knock-out mutants and a more accurate comprehension of the diatoms' cellular processes.


Human uses

File:Diatomaceous Earth BrightField.jpg,
Diatomaceous earth Diatomaceous earth (), diatomite (), or kieselgur/kieselguhr is a naturally occurring, soft, siliceous sedimentary rock that can be crumbled into a fine white to off-white powder. It has a particle size ranging from more than 3 μm to l ...
consisting of centric (radially symmetric) and pennate (bilaterally symmetric) diatoms suspended in water.
(click 3 times to fully enlarge)


Paleontology

Decomposition and decay of diatoms leads to
organic Organic may refer to: * Organic, of or relating to an organism, a living entity * Organic, of or relating to an anatomical organ Chemistry * Organic matter, matter that has come from a once-living organism, is capable of decay or is the product ...
and
inorganic In chemistry, an inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds, that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as ''inorganic chemist ...
(in the form of
silicate In chemistry, a silicate is any member of a family of polyatomic anions consisting of silicon and oxygen, usually with the general formula , where . The family includes orthosilicate (), metasilicate (), and pyrosilicate (, ). The name is a ...
s) sediment, the inorganic component of which can lead to a method of analyzing past marine environments by corings of ocean floors or
bay mud Bay mud consists of thick deposits of soft, unconsolidated silty clay, which is saturated with water; these soil layers are situated at the bottom of certain estuaries, which are normally in temperate regions that have experienced cyclical glac ...
s, since the inorganic matter is embedded in deposition of
clay Clay is a type of fine-grained natural soil material containing clay minerals (hydrous aluminium phyllosilicates, e.g. kaolin, Al2 Si2 O5( OH)4). Clays develop plasticity when wet, due to a molecular film of water surrounding the clay pa ...
s and
silt Silt is granular material of a size between sand and clay and composed mostly of broken grains of quartz. Silt may occur as a soil (often mixed with sand or clay) or as sediment mixed in suspension with water. Silt usually has a floury feel ...
s and forms a permanent geological record of such marine strata (see siliceous ooze).


Industrial

Diatoms, and their shells (frustules) as
diatomite Diatomaceous earth (), diatomite (), or kieselgur/kieselguhr is a naturally occurring, soft, siliceous sedimentary rock that can be crumbled into a fine white to off-white powder. It has a particle size ranging from more than 3 μm to le ...
or
diatomaceous earth Diatomaceous earth (), diatomite (), or kieselgur/kieselguhr is a naturally occurring, soft, siliceous sedimentary rock that can be crumbled into a fine white to off-white powder. It has a particle size ranging from more than 3 μm to l ...
, are important industrial resources used for fine polishing and liquid filtration. The complex structure of their microscopic shells has been proposed as a material for nanotechnology. Diatomite is considered to be a natural nano material and has many uses and applications such as: production of various ceramic products, construction ceramics, refractory ceramics, special oxide ceramics, for production of humidity control materials, used as filtration material, material in the cement production industry, initial material for production of prolonged-release drug carriers, absorption material in an industrial scale, production of porous ceramics, glass industry, used as catalyst support, as a filler in plastics and paints, purification of industrial waters, pesticide holder, as well as for improving the physical and chemical characteristics of certain soils, and other uses. Diatoms are also used to help determine the origin of materials containing them, including seawater.


Nanotechnology

The deposition of silica by diatoms may also prove to be of utility to
nanotechnology Nanotechnology, also shortened to nanotech, is the use of matter on an atomic, molecular, and supramolecular scale for industrial purposes. The earliest, widespread description of nanotechnology referred to the particular technological goal ...
. Diatom cells repeatedly and reliably manufacture valves of various shapes and sizes, potentially allowing diatoms to manufacture micro- or nano-scale structures which may be of use in a range of devices, including: optical systems;
semiconductor A semiconductor is a material which has an electrical conductivity value falling between that of a conductor, such as copper, and an insulator, such as glass. Its resistivity falls as its temperature rises; metals behave in the opposite way ...
nanolithography Nanolithography (NL) is a growing field of techniques within nanotechnology dealing with the engineering (patterning e.g. etching, depositing, writing, printing etc) of nanometer-scale structures on various materials. The modern term reflects on ...
; and even vehicles for
drug delivery Drug delivery refers to approaches, formulations, manufacturing techniques, storage systems, and technologies involved in transporting a pharmaceutical compound to its target site to achieve a desired therapeutic effect. Principles related to dr ...
. With an appropriate
artificial selection Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant ma ...
procedure, diatoms that produce valves of particular shapes and sizes might be evolved for cultivation in
chemostat A chemostat (from ''chem''ical environment is ''stat''ic) is a bioreactor to which fresh medium is continuously added, while culture liquid containing left over nutrients, metabolic end products and microorganisms is continuously removed at the sa ...
cultures to
mass-produce Mass production, also known as flow production or continuous production, is the production of substantial amounts of standardized products in a constant flow, including and especially on assembly lines. Together with job production and batch ...
nanoscale components. It has also been proposed that diatoms could be used as a component of solar cells by substituting
photosensitive Photosensitivity is the amount to which an object reacts upon receiving photons, especially visible light. In medicine, the term is principally used for abnormal reactions of the skin, and two types are distinguished, photoallergy and phototoxicit ...
titanium dioxide Titanium dioxide, also known as titanium(IV) oxide or titania , is the inorganic compound with the chemical formula . When used as a pigment, it is called titanium white, Pigment White 6 (PW6), or CI 77891. It is a white solid that is insolu ...
for the silicon dioxide that diatoms normally use to create their cell walls. Diatom biofuel producing solar panels have also been proposed. File:Supporting and regulating services provided by marine diatoms.png, CNN =
cloud condensation nuclei Cloud condensation nuclei (CCNs), also known as cloud seeds, are small particles typically 0.2 µm, or one hundredth the size of a cloud droplet. CCNs are a unique subset of aerosols in the atmosphere on which water vapour condenses. This c ...
, DMS =
dimethylsulphide Dimethyl sulfide (DMS) or methylthiomethane is an organosulfur compound with the formula (CH3)2S. Dimethyl sulfide is a flammable liquid that boils at and has a characteristic disagreeable odor. It is a component of the smell produced from cook ...
, DMSP =
dimethylsulfoniopropionate Dimethylsulfoniopropionate (DMSP), is an organosulfur compound with the formula (CH3)2S+CH2CH2COO−. This zwitterionic metabolite can be found in marine phytoplankton, seaweeds, and some species of terrestrial and aquatic vascular plants ...
, VOCs =
volatile organic compound Volatile organic compounds (VOCs) are organic compounds that have a high vapour pressure at room temperature. High vapor pressure correlates with a low boiling point, which relates to the number of the sample's molecules in the surrounding air, a ...
s
dashed arrow: negative effect, solid arrow: positive effects


Forensic

The main goal of diatom analysis in
forensic Forensic science, also known as criminalistics, is the application of science to criminal and civil laws, mainly—on the criminal side—during criminal investigation, as governed by the legal standards of admissible evidence and criminal p ...
s is to differentiate a death by submersion from a post-mortem immersion of a body in water. Laboratory tests may reveal the presence of diatoms in the body. Since the silica-based skeletons of diatoms do not readily decay, they can sometimes be detected even in heavily decomposed bodies. As they do not occur naturally in the body, if laboratory tests show diatoms in the corpse that are of the same species found in the water where the body was recovered, then it may be good
evidence Evidence for a proposition is what supports this proposition. It is usually understood as an indication that the supported proposition is true. What role evidence plays and how it is conceived varies from field to field. In epistemology, evidenc ...
of drowning as the
cause of death In law, medicine, and statistics, cause of death is an official determination of conditions resulting in a human's death, which may be recorded on a death certificate. A cause of death is determined by a medical examiner. The cause of death is ...
. The blend of diatom species found in a corpse may be the same or different from the surrounding water, indicating whether the victim drowned in the same site in which the body was found.


History of discovery

The first illustrations of diatoms are found in an article from 1703 in Transactions of the Royal Society showing unmistakable drawings of
Tabellaria
'. Although the publication was authored by an unnamed English gentleman, there is recent evidence that he was Charles King of Staffordshire. It is only 80 years later that we find the first formally identified diatom, the colonial ''Bacillaria paxillifera'', discovered and described in 1783 by Danish naturalist
Otto Friedrich Müller Otto Friedrich Müller, also known as Otto Friedrich Mueller (2 November 1730 – 26 December 1784) was a Danish naturalist and scientific illustrator. Biography Müller was born in Copenhagen. He was educated for the church, became tutor to a ...
. Like many others after him, he wrongly thought that it was an animal due to its ability to move. Even
Charles Darwin Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all species of life have descended ...
saw diatom remains in dust whilst in the Cape Verde Islands, although he was not sure what they were. It was only later that they were identified for him as siliceous polygastrics. The infusoria that Darwin later noted in the face paint of Fueguinos, native inhabitants of Tierra del Fuego in the southern end of South America, were later identified in the same way. During his lifetime, the siliceous polygastrics were clarified as belonging to the ''Diatomaceae'', and Darwin struggled to understand the reasons underpinning their beauty. He exchanged opinions with the noted cryptogamist G. H. K. Thwaites on the topic. In the fourth edition of On the Origin of Species he stated that "''Few objects are more beautiful than the minute siliceous cases of the diatomaceae: were these created that they might be examined and admired under the high powers of the microscope''"? and reasoned that their exquisite morphologies must have functional underpinnings rather than having been created purely for humans to admire.


See also

*
Highly branched isoprenoid Highly branched isoprenoids (HBIs) are long-chain alkenes produced by a small number of marine diatoms. There are a variety of highly branched isoprenoid structures, but C25 Highly branched isoprenoids containing 1 to 3 double bonds are the most co ...
, long-chain
alkene In organic chemistry, an alkene is a hydrocarbon containing a carbon–carbon double bond. Alkene is often used as synonym of olefin, that is, any hydrocarbon containing one or more double bonds.H. Stephen Stoker (2015): General, Organic ...
s produced by a small number of marine diatoms


Notes


References


External links


Diatom EST database
École Normale Supérieure École may refer to: * an elementary school in the French educational stages normally followed by secondary education establishments (collège and lycée) * École (river), a tributary of the Seine flowing in région Île-de-France * École, S ...

Plankton*Net
taxonomic database including images of diatom species
Life History and Ecology of Diatoms
University of California Museum of Paleontology The University of California Museum of Paleontology (UCMP) is a paleontology museum located on the campus of the University of California, Berkeley. The museum is within the Valley Life Sciences Building (VLSB), designed by George W. Kelham and ...

Diatoms: 'Nature's Marbles'
Eureka site,
University of Bergen The University of Bergen ( no, Universitetet i Bergen, ) is a research-intensive state university located in Bergen, Norway. As of 2019, the university has over 4,000 employees and 18,000 students. It was established by an act of parliament in 194 ...

Diatom life history and ecology
Microfossil Image Recovery and Circulation for Learning and Education (MIRACLE),
University College London , mottoeng = Let all come who by merit deserve the most reward , established = , type = Public research university , endowment = £143 million (2020) , budget = ...

Diatom page
,
Royal Botanic Garden Edinburgh The Royal Botanic Garden Edinburgh (RBGE) is a scientific centre for the study of plants, their diversity and conservation, as well as a popular tourist attraction. Founded in 1670 as a physic garden to grow medicinal plants, today it occupies ...

Geometry and Pattern in Nature 3: The holes in radiolarian and diatom tests


Monterey Bay Aquarium Research Institute The Monterey Bay Aquarium Research Institute (MBARI) is a private, non-profit oceanographic research center in Moss Landing, California. MBARI was founded in 1987 by David Packard, and is primarily funded by the David and Lucile Packard Founda ...

Algae image database
Academy of Natural Sciences of Philadelphia The Academy of Natural Sciences of Drexel University, formerly the Academy of Natural Sciences of Philadelphia, is the oldest natural science research institution and museum in the Americas. It was founded in 1812, by many of the leading nat ...
(ANSP)
Diatom taxa
Academy of Natural Sciences of Philadelphia The Academy of Natural Sciences of Drexel University, formerly the Academy of Natural Sciences of Philadelphia, is the oldest natural science research institution and museum in the Americas. It was founded in 1812, by many of the leading nat ...
(ANSP)
An Introduction to the Microscopical Study of Diatoms
by Robert B. McLaughlin {{Authority control Algae classes *