View source for Diatom

{{for|a molecule of two atoms|Diatomic molecule}}

{{Taxobox
| color = greenyellow
| name = Diatoms
| image = Diatom2.jpg
| image_width = 250px
| image_caption = Marine diatoms
| domain = [[Eukaryote|Eukaryota]]
| kingdom = [[Chromalveolata]]
| unranked_regnum = [[SAR supergroup]]
| phylum = [[Heterokont]]ophyta
| classis = '''Bacillariophyceae'''
| classis_authority = [[Pierre Dangeard|Dangeard]], 1933<ref>Dangeard, P. (1933). ''Traite d'Algologie.'' Paul Lechvalier and Fils, Paris, [https://books.google.com/books?id=mDxVAAAAMAAJ].</ref>
| subdivision_ranks = [[Order (biology)|Orders]]
see text
| synonyms = 
* Diatomea <small>[[Barthélemy Charles Joseph Dumortier|Dumortier]], 1821</small><ref>Dumortier, B.-C. (1822). ''[http://images.algaebase.org/pdf/AC100CF013cd51B91ERyQ180397B/16499.pdf Commentationes botanicae. Observations botaniques, dédiées à la Société d'Horticulture de Tournay]'' (disponible at Algaebase). pp. [i], [1]-116, [1, tabl., err.]. Tournay: Imprimerie de Ch. Casterman-Dieu, Rue de pont No. 10.</ref>
* Diatomophyceae <small>[[Gottlob Ludwig Rabenhorst|Rabenhorst]], 1864</small><ref>Rabenhorst, L. ''[https://archive.org/details/floraeuropaeaalg0103rabe Flora europaea algarum aquae dulcis et submarinae]'' (1864-1868). ''Sectio I. Algas diatomaceas complectens, cum figuris generum omnium xylographice impressis'' (1864). pp. 1-359. Lipsiae [Leipzig]: Apud Eduardum Kummerum.</ref>
* Bacillariae <small>Haeckel, 1878</small><ref>Haeckel, E. (1878). ''[http://caliban.mpipz.mpg.de/haeckel/protistenreich/high/IMG_8499.html Das Protistenreich].''</ref>
* Bacillariophyta <small>[[Engler system|Engler & Gilg]], 1919</small><ref>Engler, A. & Gilg, E. (1919). ''Syllabus der Pflanzenfamilien: eine Übersicht über das gesamte Pflanzensystem mit besonderer Berücksichtigung der Medizinal- und Nutzpflanzen, nebst einer Übersicht über die Florenreiche und Florengebiete der Erde zum Gebrauch bei Vorlesungen und Studien über spezielle und medizinisch-pharmazeutische Botanik'', 8th ed., Gebrüder Borntraeger Verlag, Berlin, 395 p.</ref>
}}
'''Diatoms'''<ref>{{LSJ|dia/tomos|''diá-tom-os''}} "cut in half" (= [http://www.perseus.tufts.edu/hopper/text?doc=Perseus%3Atext%3A1999.04.0058%3Aalphabetic+letter%3D*d%3Aentry+group%3D30%3Aentry%3Ddixo%2Ftomos ''dichó-tom-os'']) — {{LSJ|dia/|''diá''}} "through" or "apart" and the root of {{LSJ|te/mnw1|''tém-n-ō''}} "I cut". {{ablaut|e|o||verb root}}</ref> are a major group of [[algae]], and are among the most common types of [[phytoplankton]].  Diatoms are [[unicellular]], although they can form [[Colony (biology)|colonies]] in the shape of filaments or ribbons (e.g. ''Fragilaria''), fans (e.g. ''Meridion''), zigzags (e.g. ''[[Tabellaria]]''), or stars (e.g. ''[[Asterionella]]''). The first diatom formally described in scientific literature, the colonial ''[[Bacillaria paxillifer|Bacillaria paradoxa]]'', was found in 1783 by Danish naturalist [[Otto Friedrich Müller]]. Diatoms are [[Autotroph|producers]] within the [[food chain]].  A unique feature of diatom cells is that they are enclosed within a cell wall made of [[silica]] (hydrated silicon dioxide) called a [[frustule]].<ref>{{cite web | title=More on Diatoms | website=University of California Museum of Paleontology | url = http://www.ucmp.berkeley.edu/chromista/diatoms/diatommm.html}}</ref> These frustules show a wide diversity in form, but are usually almost bilaterally symmetrical, hence the group name. The symmetry is not perfect since one of the valves is slightly larger than the other, allowing one valve to fit inside the edge of the other. [[Fossil]] evidence suggests that they originated during, or before, the early [[Jurassic period]]. Only male gametes of centric diatoms are capable of movement by means of [[flagellum|flagella]]. Diatom communities are a popular tool for [[environmental monitoring|monitoring environmental]] conditions, past and present, and are commonly used in studies of water quality.

==General biology==<!-- This section is linked from [[Frustule]] -->
[[File:20110123 185042 Diatom.jpg|thumb|255px|A diatom.&nbsp; Numbered graduations are 10 micrometres apart]]

There are more than 200 [[genus|genera]] of living diatoms, and it is estimated that there are approximately 100,000 [[Extant taxon|extant]] [[species]].<ref name="HasleSyvertsen1996">{{cite book|author1=Grethe R. Hasle|author2=Erik E. Syvertsen |author3=Karen A. Steidinger |author4=Karl Tangen|editor=Carmelo R. Tomas|title=Identifying Marine Diatoms and Dinoflagellates|url=http://books.google.com/books?id=KQxPtwonlqoC|accessdate=2013-11-13|date=1996-01-25|publisher=Academic Press|isbn=978-0-08-053441-1|pages=5–385|chapter=Marine Diatoms}}</ref><ref name="RoundCrawford1990">{{cite book|author1=Frank Eric Round|author2=R. M. Crawford|author3=D. G. Mann|title=The Diatoms: Biology & Morphology of the Genera|url=http://books.google.com/books?id=xhLJvNa3hw0C|accessdate=2013-11-13|year=1990|publisher=Cambridge University Press|isbn=978-0-521-36318-1}}</ref><ref name="Lund95">Canter-Lund, H. and Lund, J.W.G. (1995). ''Freshwater Algae: Their microscopic world explained'', Biopress Limited. ISBN 0-948737-25-5.</ref><ref>{{cite journal | last =Mann | first =David G. | title = The species concept in diatoms: Evidences for morphologically distinct, sympatric gamodemes in four epipelic speices | journal =Plant Systematics and Evolution | volume =164 | issue =1–4 | pages =215–237 | publisher =Springer Science+Business Media | year =1989 | url =http://www.springerlink.com/content/n307k3757002213t/|  issn =1615-6110 | doi =10.1007/BF00940439 | accessdate = 2013-11-13}}</ref>  Diatoms are a widespread group and can be found in the [[ocean]]s, in [[freshwater]], in [[soil]]s and on damp surfaces. Most live [[pelagic]]ally in open water, although some live as surface films at the water-sediment interface ([[benthos|benthic]]), or even under damp atmospheric conditions. They are especially important in oceans, where they are estimated to contribute up to 45% of the total oceanic [[primary production]] of organic material.<ref name="BGCC1">{{cite journal | url=http://www.soes.soton.ac.uk/staff/tt/pdfs/silica.pdf | title=Role of diatoms in regulating the ocean's silicon cycle | author=Yool, Andrew; Tyrrell, Toby | journal=Global Biogeochemical Cycles | year=2003 | volume=17 | issue=4 | pages=1103–1124 | doi=10.1029/2002GB002018|bibcode = 2003GBioC..17.1103Y }}</ref><!-- Mann (1989) does not mention this; moved this citation upward --- mmm, it's in Mann (1999) --> Spatial distribution of marine phytoplankton species is restricted both horizontally and vertically.<ref>{{cite journal|doi=10.2307/2406711|last=Lipps|first=J.H.|year=1970|title=Plankton Evolution|jstor=2406711|journal= Diatoms occur in all oceans from the poles to the tropics; polar and subpolar regions contain relatively few species compared with temperate biota. Although tropical regions exhibit the greatest number of species, more abundant populations are found in polar to temperate regions.|pages=1–22|volume=24|issue=1}}</ref><ref name="Horner2002">{{cite book|author=Rita A. Horner|title=A taxonomic guide to some common marine phytoplankton|url=http://books.google.com/books?id=JU8VAQAAIAAJ|accessdate=2013-11-13|year=2002|publisher=Biopress|isbn=978-0-948737-65-7|pages=25–30}}</ref>  Though usually [[microscope|microscopic]], some species of diatoms can reach up to 2 millimeters in length.

[[File:Diatomeas w.jpg|thumb|300px|right|Several species of fresh-water diatoms.]]

Diatoms belong to a large group called the [[heterokont]]s, including both [[autotroph]]s (''e.g.'', [[golden alga]]e, [[kelp]]) and [[heterotroph]]s (''e.g.'', [[water mould]]s). Their yellowish-brown [[chloroplast]]s are typical of heterokonts, having four [[plasma membrane|membranes]] and containing [[biological pigment|pigments]] such as the [[carotenoid]] [[fucoxanthin]]. Individuals usually lack [[flagellum|flagella]], but they are present in male [[gamete]]s of the centric diatoms and have the usual heterokont structure, except they lack the hairs ([[mastigonemes]]) characteristic in other groups. Most diatoms are [[Motility|non-motile]], as their relatively dense cell walls cause them to readily sink. Planktonic forms in open water usually rely on [[turbulence|turbulent]] mixing of the upper layers by the [[wind]] to keep them suspended in sunlit surface waters. Some species actively regulate their buoyancy with intracellular [[lipid]]s to counter sinking.

A feature of diatoms is the [[urea cycle]], which links them evolutionarily to animals. This was discovered in research carried out by Andrew Allen, Chris Bowler and colleagues. Their findings, published in 2011, that diatoms have a functioning urea cycle was highly significant, since prior to this the urea cycle was thought to have originated with the [[metazoans]] who appeared several hundreds of millions of years after the diatoms. Their study showed that while diatoms and animals use the urea cycle for different ends, they are seen to be evolutionally linked in such a way that animals and plants are not.<ref>{{Cite web | title =Animal-Like Urea Cycle in Ocean's Tiny Diatoms Enables Marine Phytoplankton to Use Carbon and Nitrogen from Their Environment | work =Science Daily | section = Science News | publisher =Science Daily | date =2011-05-12 | url =http://www.sciencedaily.com/releases/2011/05/110511133553.htm | accessdate = 2013-11-13}}</ref>

Diatom cells are contained within a unique silica [[cell wall]] comprising two separate valves (or shells).{{citation needed|date=January 2016}} The [[biogenic silica]] composing the cell wall is synthesised [[intracellular]]ly by the [[polymerisation]] of [[silicic acid]] [[monomer]]s. This material is then extruded to the cell exterior and added to the wall. Diatom cell walls are also called [[frustule]]s or "tests", and their two valves typically overlap one over the other like the two halves of a [[petri dish]]. 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]]. This expands in size to give rise to a much larger cell, which then returns to size-diminishing divisions.{{citation needed|date=January 2016}} Auxospore production is almost always linked to [[meiosis]] and sexual reproduction.

Decomposition and decay of diatoms leads to [[organic matter|organic]] and [[inorganic]] (in the form of [[silicate]]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]]s, since the inorganic matter is embedded in deposition of [[clay]]s and [[silt]]s and forms a permanent [[geological]] record of such marine strata. (See [[siliceous ooze]]).

The study of diatoms is a branch of [[phycology]], and phycologists specializing in diatoms are called diatomists.

==Classification==
[[File:Diatomeas-Haeckel.jpg|thumb|right|Selections from [[Ernst Haeckel]]'s 1904 ''[[Kunstformen der Natur]]'' (Art Forms of Nature), showing pennate (left) and centric (right) frustules.]]
[[File:Diatomaceous Earth BrightField.jpg|thumb|right|300px|[[Diatomaceous earth]] as viewed under [[bright field microscopy|bright field]] [[lighting|illumination]] on a [[light microscope]]. Diatomaceous earth is a soft, [[siliceous]], [[sedimentary rock]] made up of the [[cell walls]] of [[diatoms]] and readily crumbles to a fine powder. This sample consists of a mixture of centric (radially symmetric) and pennate (bilaterally symmetric) diatoms. This image of diatomaceous earth particles in [[water]] is at a scale of 6.236 pixels/[[μm]], the entire image covers a region of approximately 1.13 by 0.69 mm.]]

The classification of heterokonts is still unsettled, and they may be treated as a [[Division (biology)|division]] (or [[Phylum (biology)|phylum]]), [[Kingdom (biology)|kingdom]], or something in-between. Accordingly, groups like the diatoms may be ranked anywhere from class (usually called '''Diatomophyceae''' or '''Bacillariophyceae''') to division (usually called '''Bacillariophyta'''), with corresponding changes in the ranks of their subgroups.

Diatoms are traditionally divided into two [[Order (biology)|orders]]:
* '''centric''' diatoms ([[Centrales]]), which are radially [[symmetry|symmetrical]]
* '''pennate''' diatoms ([[Pennales]]), which are bilaterally symmetrical. The former are [[paraphyletic]] to the latter.

Due to the difference noted in pennate diatoms, of the presence or absence of a raphe (a longitudinal groove in the valve),<ref>O.E.D. 2nd edition 2005</ref> a more recent classification by Round, Crawford & Mann (1990)<ref name="RoundCrawford1990"/> divides the diatoms (as Bacillarophyta) into three classes and a number of orders:<ref>{{cite web | title =Bacillariophyceae | work =algaebase | publisher =M. D. Guiry | url =http://www.algaebase.org/browse/taxonomy/?id=4337 | accessdate = 2013-11-11}}</ref>

*Class [[Coscinodiscophyceae]] Round & R.M.Crawford:<br>centric diatoms
** [[Anaulales]] Round & R.M.Crawford
** [[Arachnoidiscales]] Round
** [[Asterolamprales]] Round
** [[Aulacoseirales]] R.M.Crawford
** [[Biddulphiales]]
** [[Chaetocerotales]] Round & R.M.Crawfor
** [[Chrysanthemodiscales]] Round
** [[Corethrales]] Round & R.M.Crawford
** [[Coscinodiscales]] Round
** [[Cymatosirales]] Round & R.M.Crawford
** [[Ethmodiscales]] Round
** [[Hemiaulales]] Round & R.M.Crawford
** [[Leptocylindrales]] Round & R.M.Crawford
** [[Lithodesmiales]]
** [[Melosirales]] R.M.Crawford
** [[Orthoseirales]] R.M.Crawford
** [[Paraliales]] R.M.Crawford
** [[Rhizosoleniales]]
** [[Stictocyclales]] Round
** [[Stictodiscales]] Round & R.M.Crawford
** [[Thalassiosirales]]
** [[Triceratiales]] Round & R.M.Crawford
 {{Col-begin}}
 {{Col-1-of-2}}
* Class [[Fragilariophyceae]] F.E.Round:<br>pennate diatoms without a [[raphe]] (araphids)
** [[Ardissoneales]] F.E.Round
** [[Climacospheniales]] Round
** [[Cyclophorales]] Round & R.M.Crawford
** [[Fragilariales]] P.C.Silva
** [[Licmophorales]] Round
** [[Protoraphidales]] Round
** [[Rhabdonematales]] Round & R.M.Crawford
** [[Rhaphoneidales]] Round
** [[Striatellales]] F.E.Round
** [[Tabellariales]] Round
** [[Thalassionematales]] Round
** [[Toxariales]] Round
 {{Col-2-of-2}}
* Class [[Bacillariophyceae]] Haeckel, 1878, ''emend.'' D.G.Mann:<br>pennate diatoms with a raphe (raphids)
** [[Achnanthales]] P.C.Silva
** [[Bacillariales]] Hendey
** [[Cymbellales]] D.G.Mann
** [[Dictyoneidales]] D.G.Mann
** [[Eunotiales]] P.C.Silva
** [[Lyrellales]] D.G.Mann
** [[Mastogloiales]] D.G.Mann
** [[Naviculales]] Bessey
** [[Rhopalodiales]] D.G.Mann
** [[Surirellales]] D.G.Mann
** [[Thalassiophysales]] D.G.Mann
 {{Col-end}}
It is probable there will be further revisions as understanding of their relationships increases. Medlin & Kaczmarska (2004) propose the following classification for the diatoms:<ref>{{cite journal | last =Medlin | first =Linda K. | last2 =Kaczmarska | first2 =Irena | title =Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision | journal =Phycologia | volume =43 | issue =3 | pages =245–270 | publisher =International Phycological Society | year =2004 | url =http://epic.awi.de/12139/1/Med2004a.pdf | doi =10.2216/i0031-8884-43-3-245.1 | accessdate = 2013-11-13}}</ref>

* Bacillaryophyta
** Coscinodiscophytina
*** Coscinodiscophyceae ('radial centrics')
** Bacillariophytina 
*** Mediophyceae ('polar centrics')
*** Bacillariophyceae (pennate diatoms)

Diatoms generally range in size from 2 to 200μm,<ref name="HasleSyvertsen1996"/> and build intricate hard but porous cell walls (called [[frustule]]s or [[Test (biology)|tests]]) composed primarily of [[silica]].<ref name="Horner2002"/>{{rp|25–30}}  This siliceous wall<ref name=CMoG>{{cite web|title=Glass in Nature|url=http://www.cmog.org/article/glass-nature|publisher=The Corning Museum of Glass|accessdate=19 February 2013}}</ref>  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 [[Frustule#Thecae|epitheca]]. Diatom morphology varies. Although the shape of the cell is typically circular, some cells may be triangular, square, or elliptical.

Cells are solitary or united into colonies of various kinds, which may be linked by siliceous structures; [[marine mucilage|mucilage]] pads, stalks or tubes; amorphous masses of mucilage, or by threads of [[chitin]], (polysaccharide) which are secreted through strutted processes of the cell. Major pigments of diatoms are [[chlorophylls]] a and c, [[beta-carotene]], [[fucoxanthin]], diatoxanthin and diadinoxanthin.<ref name="HasleSyvertsen1996"/>  Diatoms are mainly photosynthetic. A few, however, are obligate [[heterotrophs]], while others can live heterotrophically in the absence of light, provided an appropriate organic carbon source is available.  Storage products are [[chrysolaminarin]] and [[lipids]].<ref name="Horner2002"/>

[[Hoek, Mann and Jahns system|Hoek ''et al.'' (1995)]]<ref name="Hoek1995">{{cite book|author1=Christiaan Van Den Hoek|author2=D. G. Mann|author3=H. M. Jahns|title=Algae: An Introduction to Phycology|url=http://books.google.com/books?id=xuUoiFesSHMC|accessdate=2013-11-13|year=1995|publisher=Cambridge University Press|isbn=978-0-521-31687-3}}</ref> also provide a comprehensive coverage of diatom taxonomy.

==Ecology==
[[File:Oceanic Silicon Cycle Budget.svg|thumb|350px|right|A budget of the ocean's silicon cycle<ref name="AAAS1">{{cite journal | last =Tréguer | first =Paul | last2 =Nelson | first2 =David M. | last3 =Van Bennekom | first3 =Aleido J. | last4 =DeMaster | first4 =David J. | last5 =Leynaert | first5 =Aude | last6 =Quéguiner | first6 =Bernard | title =The Silica Balance in the World Ocean: A Reestimate | journal =Science | volume =268 | issue =5209 | pages =375–379 | publisher =American Association for the Advancement of Science | year =1995 | url =http://www.sciencemag.org/content/268/5209/375.abstract | doi =10.1126/science.268.5209.375 | accessdate = 2013-11-13 | pmid =17746543|bibcode = 1995Sci...268..375T }}</ref>]]
[[File:Diatoms+Abundance.png|thumb|300px|right|Regions of high abundance of Diatoms in the ocean]]

[[Plankton]]ic diatoms in freshwater and marine environments typically exhibit a "[[boom and bust]]" (or "'''bloom''' and bust") lifestyle. When conditions in the upper mixed layer (nutrients and light) are favourable (''e.g.'' at the start of spring) their competitive edge<ref name=furnas90>{{cite journal | last =Furnas | first =Miles J. | title =In situ growth rates of marine phytoplankton: approaches to measurement, community and species growth rates | journal =Journal of Plankton Research | volume =12 | issue =6 | pages =1117–1151 | publisher =Oxford Journals | url =http://plankt.oxfordjournals.org/content/12/6/1117.abstract#5085 | doi =10.1093/plankt/12.6.1117 | accessdate = 2013-11-14 | year =1990}}</ref> allows them to quickly dominate phytoplankton communities ("boom" or "bloom"). As such they are often classed as opportunistic [[r-selection|r-strategists]] (''i.e.'' those organisms whose ecology is defined by a high growth rate, ''r'').

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 species is native to Europe and is an invasive alien both in the antipodes and in parts of  North America.<ref>[http://alienspecies.royalbcmuseum.bc.ca/eng/species/didymo-rock-snot Didymo, Aliens Among Us.] Virtual Exhibit of the [[Virtual Museum of Canada]]</ref><ref>[http://www.ct.gov/deep/cwp/view.asp?A=4013&Q=476204 DEP Reports Didymo Discovered in the West Branch Farmington River. Retrieved on 2014-01-15.]</ref>  The problem is most frequently recorded from Australia and [[Didymo in New Zealand|New Zealand]].<ref>{{cite web |url=http://www.biosecurity.govt.nz/pests/didymo/update-31-10-08| title=Didymo Stakeholder Update - 31 October 2008 | publisher=MAF Biosecurity New Zealand www.biosecurity.govt.nz | accessdate=2013-12-01 }}</ref>

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]]). 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]].

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]]<ref name=dugdale98>{{cite journal | last1 = Dugdale | first1 = R. C. | last2 = Wilkerson | first2 = F. P. | year = 1998 | title = Silicate regulation of new production in the equatorial Pacific upwelling | url = http://www.nature.com/nature/journal/v391/n6664/abs/391270a0.html | journal = Nature | volume = 391 | issue = 6664| pages = 270–273 | doi=10.1038/34630|bibcode = 1998Natur.391..270D }}</ref>), 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 condition that typically causes diatom (spring) blooms to end is a lack of silicon. Unlike other nutrients, this is a major requirement solely of diatoms, so it is not regenerated in the plankton ecosystem as efficiently as, for instance, [[nitrogen]] or [[phosphorus]] 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<ref name=dugdale98/><ref name=smetacek85>{{cite journal | last1 = Smetacek | first1 = V. S. | year = 1985 | title = Role of sinking in diatom life-history cycles: Ecological, evolutionary and geological significance | url = http://www.springerlink.com/content/t5g25521p5252014/ | journal = Mar Biol. | volume = 84 | issue = 3| pages = 239–251 | doi = 10.1007/BF00392493 }}</ref> (see also the [[biological pump]]). Significantly, they also play a key role in the regulation of the biogeochemical cycle of [[silicon]] in the modern ocean.<ref name="BGCC1"/><ref name="AAAS1"/>

[[File:Diatoms Egge and Aksnes 1992 plot.png|thumb|300px|right|Egge & Aksnes (1992)<ref name=egge92>{{cite journal | last1 = Egge | first1 = J. K. | last2 = Aksnes | first2 = D. L. | year = 1992 | title = Silicate as regulating nutrient in phytoplankton competition | url = http://www.int-res.com/articles/meps/83/m083p281.pdf | format = PDF | journal = Mar Ecol. Prog. Ser. | volume = 83 | issue = | pages = 281–289 | doi = 10.3354/meps083281 }}</ref> figure.]]

The use of silicon by diatoms is believed by many researchers to be the key to their ecological success. In a now classic study, Egge and Aksnes (1992)<ref name=egge92/> found that diatom dominance of mesocosm communities was directly related to the availability of silicic acid — when concentrations were greater than 2 [[Mole (unit)|µmol]] m<sup>−3</sup>, they found that diatoms typically represented more than 70% of the phytoplankton community. Raven (1983)<ref name=raven83>{{cite journal | last1 = Raven | first1 = J. A. | year = 1983 | title = The transport and function of silicon in plants | url = | journal = Biol. Rev. | volume = 58 | issue = 2| pages = 179–207 | doi=10.1111/j.1469-185X.1983.tb00385.x}}</ref> noted that, relative to organic cell walls, silica frustules require less energy to synthesize (approximately 8% of a comparable organic wall), potentially a significant saving on the overall cell energy budget. Other researchers<ref name=milligan02>{{cite journal | last1 = Milligan | first1 = A. J. | last2 = Morel | first2 = F. M. M. | year = 2002 | title = A proton buffering role for silica in diatoms | url = http://www.sciencemag.org/cgi/content/full/297/5588/1848 | journal = Science | volume = 297 | issue = 5588| pages = 1848–1850 | doi=10.1126/science.1074958 | pmid=12228711|bibcode = 2002Sci...297.1848M }}</ref> have suggested that the biogenic silica in diatom cell walls acts as an effective [[pH]] [[buffering agent]], facilitating the conversion of [[bicarbonate]] to dissolved CO<sub>2</sub> (which is more readily assimilated). Notwithstanding the possible advantages conferred by silicon, diatoms typically have higher growth rates than other algae of a corresponding size.<ref name=furnas90/>

Diatoms occur in virtually every environment that contains water. This includes not only oceans, seas, lakes and streams, but also soil.

==Life-cycle==
[[File:Centric diatom life-cycle.jpg|thumb|200px|Sexual reproduction of a centric diatom ([[oogamy]])]]
[[File:Diatom pennate life cycle.jpg|thumb|200px|Sexual reproduction of a pinnate diatom (morphological [[isogamy]], physiological [[anisogamy]])]]

Reproduction among these organisms is primarily asexual by binary fission, with each daughter cell receiving one of the parent cell's two [[frustule]]s (or [[theca]]).  This is used by each daughter cell as the larger frustule (or epitheca) into which a second, small frustule (or hypotheca) is constructed.

This form of division results in a size reduction of the daughter cell that received the smaller frustule from the parent and therefore the average cell size of a diatom population decreases, until the cells are about one-third their maximum size.<ref name="HasleSyvertsen1996"/> It has been observed, however, that certain taxa have the ability to divide without causing a reduction in cell size.<ref name="Werner1977">{{cite book|author=G. Drebes|editor=Dietrich Werner|title=The Biology of Diatoms|url=http://books.google.com/books?id=A4GBA7rlAroC|accessdate=2013-11-14|volume=Volume 13 of Botanical Monographs|date=1 January 1977|publisher=University of California Press|isbn=978-0-520-03400-6|pages=250–283|chapter=Chapter 9: Sexuality}}</ref> Nonetheless, in order to restore the cell size of a diatom population for those that do endure size reduction, sexual reproduction and [[auxospore]] formation must occur.<ref name="HasleSyvertsen1996"/> Vegetative cells of diatoms are [[diploid]] (2N) and so [[meiosis]] can take place, producing male and female gametes which then fuse to form the [[zygote]]. 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.<ref name="Horner2002"/>

Diatoms are mostly [[Motility|non-motile]]; however, sperm found in some species can be [[Flagellum|flagellated]], though motility is usually limited to a gliding motion.<ref name="Horner2002"/>  In centric diatoms, the small male [[gametes]] have one [[flagellum]] while the female gametes are large and non-motile ([[Oogamy|oogamous]]). Conversely, in pennate diatoms both gametes lack flagella ([[isogamy|isoogamous]]).<ref name="HasleSyvertsen1996"/>  Certain araphid species, that is pennate diatoms without a raphe, have been documented as anisogamous and are, therefore, considered to represent a transitional stage between centric and raphid pennate diatoms, diatoms with a raphe.<ref name="Werner1977"/>

==Evolutionary history==
Heterokont chloroplasts appear to be derived from those of [[red algae]], rather than directly from [[prokaryote]]s as occurred in [[plant]]s. This suggests they had a more recent origin than many other algae. However, fossil evidence is scant, and it is really only with the evolution of the diatoms themselves that the heterokonts make a serious impression on the fossil record.

The earliest known fossil diatoms date from the early [[Jurassic]] (~185 [[Mega-annum|Ma ago]]),<ref name=kooistra96>{{cite journal | last =Kooistra | first =W. H. C. F. | last2 =Medlin | first2 =L. K. | title =Evolution of the Diatoms (Bacillariophyta) IV A Reconstruction of Their Age from Small Subunit rRNA Coding Regions and the Fossil Record | journal =Molecular Phylogenetics and Evolution | volume =6 | issue =3 | pages =391–407 | publisher =Academic Press | year =1996 | url =http://www.ingentaconnect.com/content/ap/fy/1996/00000006/00000003/art00088 | accessdate = 2013-11-14 | doi =10.1006/mpev.1996.0088 | pmid =8975694}}</ref>  although the [[molecular clock]]<ref name=kooistra96/> and [[sedimentary rock|sedimentary]]<ref name=schieber00>{{cite journal | last =Schieber | first =Jürgen | last2 =Krinsley | first2 =Dave | last3 =Riciputi | first3 =Lee | title =Diagenic origin of quartz silt in mudstones and implications for silica cycling | journal =Nature | volume =406 | pages =981–985 | publisher =Nature Publishing Group | year =2000 | url =http://www.nature.com/nature/journal/v406/n6799/abs/406981a0.html | issn =0028-0836 | doi =10.1038/35023143 | pmid =10984049| accessdate = 2013-11-14 | issue =6799}}</ref> evidence suggests an earlier origin. It has been suggested that their origin may be related to the [[Permian–Triassic extinction event|end-Permian mass extinction]] (~250 Ma), after which many marine [[ecological niche|niche]]s were opened.<ref name=medlin97>{{cite journal | last1 = Medlin | first1 = L. K. | last2 = Kooistra | first2 = W. H. C. F. | last3 = Gersonde | first3 = R. | last4 = Sims | first4 = P. A. | last5 = Wellbrock | first5 = U. | year = 1997 | title = Is the origin of the diatoms related to the end-Permian mass extinction? | url = | journal = Nova Hedwegia | volume = 65 | issue = | pages = 1–11 }}</ref>  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 (zoology)|cryptic]].<ref name=raven04>{{cite journal | last1 = Raven | first1 = J. A. | last2 = Waite | first2 = A. M. | year = 2004 | title = The evolution of silicification in diatoms: inescapable sinking and sinking as escape? | url = http://www.blackwell-synergy.com/doi/abs/10.1111/j.1469-8137.2004.01022.x | journal = New Phytologist | volume = 162 | issue = | pages = 45–61 | doi=10.1111/j.1469-8137.2004.01022.x}}</ref>  Since the advent of silicification, diatoms have made a significant impression on the fossil record, with major deposits of fossil diatoms found as far back as the early [[Cretaceous]], and some rocks ([[diatomaceous earth]], diatomite, kieselguhr) being composed almost entirely of them.

Although the diatoms may have existed since the [[Triassic]], the timing of their ascendancy and "take-over" of the silicon cycle is more recent. Prior to the [[Phanerozoic]] (before 544 Ma), it is believed that [[bacteria|microbial]] or [[inorganic]] processes weakly regulated the ocean's silicon cycle.<ref name="SchneiderBoston1993">{{cite book|author1=R. Siever|author2=Stephen Henry Schneider|author3=Penelope J. Boston|title=Scientists on Gaia|url=http://books.google.com/books?id=h83nGwAACAAJ|accessdate=2013-11-14|date=January 1993|publisher=Mit Press|isbn=978-0-262-69160-4|pages=287–295|chapter=Silica in the oceans: biological-geological interplay}}</ref><ref>{{cite journal |last = Kidder | first = David L. | last2 =Erwin | title =Secular Distribution of Biogenic Silica through the Phanerozoic: Comparison of Silica-Replaced Fossils and Bedded Cherts at the Series Level | journal =The Journal of Geology | volume =109 | issue =4 | pages =509–522 | publisher =The University of Chicago Press | year =2001 | doi =10.1086/320794 | jstor =320794 | first2 =Douglas H. | bibcode=2001JG....109..509K}}</ref><ref name=grenne03>{{cite journal | last1 = Grenne | first1 = T. | last2 = Slack | first2 = J. F. | year = 2003 | title = Paleozoic and Mesozoic silica-rich seawater: evidence from hematitic chert (jasper) deposits | url = http://geology.geoscienceworld.org/cgi/content/abstract/31/4/319 | journal = Geology | volume = 31 | issue = 4| pages = 319–322 |bibcode = 2003Geo....31..319G |doi = 10.1130/0091-7613(2003)031<0319:PAMSRS>2.0.CO;2 | issn = 0091-7613 }}</ref>  Subsequently, the cycle appears dominated (and more strongly regulated) by the [[radiolaria]]ns and [[sea sponge|siliceous sponges]], the former as [[zooplankton]], the latter as [[sedentary lifestyle|sedentary]] [[filter feeder]]s primarily on the [[continental shelf|continental shelves]].<ref>{{cite journal | last =Racki | first =Grzegorz | last2 =Cordey | first2 =Fabrice | title =Radiolarian palaeocology and radiolarites: is the present the key to the past? | journal =Earth-Science Reviews | volume =52 | issue =1–3 | pages =83–120 | publisher =Elsevier B. V. | year =2000 | url =http://www.sciencedirect.com/science/article/pii/S0012825200000246 | accessdate = 2013-11-14 | doi =10.1016/S0012-8252(00)00024-6 | bibcode=2000ESRv...52...83R}}</ref>  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" is unclear, and different authors have conflicting interpretations of the fossil record. Some evidence, such as the displacement of siliceous sponges from the shelves,<ref name=maldonado99>{{cite journal | last1 = Maldonado | first1 = M. | last2 = Carmona | first2 = M. C. | last3 = Uriz | first3 = J. M. | last4 = Cruzado | first4 = A. | year = 1999 | title = Decline in Mesozoic reef-building sponges explained by silicate limitation | url = http://www.nature.com/nature/journal/v401/n6755/abs/401785a0.html | journal = Nature | volume = 401 | issue = 6755| pages = 785–788 | doi=10.1038/44560|bibcode = 1999Natur.401..785M }}</ref> suggests that this takeover began in the Cretaceous (146 Ma to 65 Ma), while evidence from radiolarians suggests "take-over" did not begin until the [[Cenozoic]] (65 Ma to present).<ref>{{cite journal | last =Harper | first =Howard E., Jr. | title =Silica, diatoms, and Cenozoic radiolarian evolution | journal =Geology | volume =3 | issue =4 | pages =175 | publisher =The Geological Society of America | year =1975 | url =http://mr.crossref.org/iPage?doi=10.1130%2F0091-7613%281975%293%3C175%3ASDACRE%3E2.0.CO%3B2 | doi =10.1130/0091-7613(1975)3<175:SDACRE>2.0.CO;2 | accessdate = 2013-11-11 | issn =0091-7613 | first2 =Andrew H.| last2 =Knoll |bibcode = 1975Geo.....3..175H }}</ref>  The expansion of [[grassland]] [[biome]]s and the [[evolutionary radiation]] of [[grass]]es during the [[Miocene]] is believed to have increased the flux of soluble silicon to the oceans, and it has been argued that this has promoted the diatoms during the Cenozoic era.<ref>{{cite journal |last=Falkowski |first=P.G. |year=2004 |title=The evolution of modern eukaryotic phytoplankton |journal=Science |volume=305 |pages=354–60 |doi=10.1126/science.1095964 |pmid=15256663 |issue=5682 |bibcode = 2004Sci...305..354F |last3=Knoll |first3=Andrew H. |last4=Quigg |first4=Antonietta |last5=Raven |first5=John A. |last6=Schofield |first6=Oscar |last7=Taylor |first7=F. J. R. |display-authors=etal}}</ref><ref>{{cite journal |last=Kidder |first=D.L. |author2=Gierlowski-Kordesch, E.H. |year=2005 |title=Impact of grassland radiation on the nonmarine silica cycle and Miocene diatomite |journal=PALAIOS |volume=20 |pages=198–206 |doi=10.2110/palo.2003.p03-108 |issue=2 }}</ref>  Recent work suggests that diatom success is decoupled from the evolution of grasses, although both diatom and grassland diversity increased strongly since the middle Miocene.<ref name="Lazarus2014">{{cite journal |last=Lazarus |first=D.|year=2014 |title=Cenozoic planktonic marine diatom diversity and correlation to climate change |journal=PLoS ONE  |volume=9 |pages=1–18 |doi=10.1371/journal.pone.0084857 |last3=Renaudie|first3=Johan|last4=Diver|first4=Patrick|last5=Türke|first5=Andreas|bibcode = 2014PLoSO...984857L |display-authors=etal}} {{open access}}</ref>  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, projected in global warming scenarios,<ref>IPCC Core Writing Team, 2007. Climate Change 2007: Synthesis Report. 104.</ref> 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.<ref name="Lazarus2014"/>

==Fossil record==
[[File:Paralia sulcata diatom.tif|thumb|250px|''Paralia sulcata'' diatom imaged using the University of Tasmania scanning electron microscope.]]
The fossil record of diatoms has largely been established through the recovery of their siliceous [[frustule]]s in marine and non-marine sediments. Although diatoms have both a marine and non-marine stratigraphic record, diatom [[biostratigraphy]], 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.<ref name=Scherer07>Scherer, R.P., Gladenkov, A.Yu., and  Barron, J.A. (2007). Methods and applications of Cenozoic marine diatom biostratigraphy. "Paleontological Society Papers" '''13''', 61–83</ref> Where diatom [[biozone]]s are well established and calibrated to the [[geomagnetic polarity time scale]] (e.g., [[Southern Ocean]], [[North Pacific]], eastern equatorial [[Pacific]]), diatom-based age estimates may be resolved to within <100,000 years, although typical age resolution for [[Cenozoic]] diatom assemblages is several hundred thousand years.

The [[Cretaceous]] record of diatoms is limited, but recent studies reveal a progressive diversification of diatom types. The [[Cretaceous–Paleogene extinction event]], which in the oceans dramatically affected organisms with calcareous skeletons, appears to have had relatively little impact on diatom evolution.<ref name=Harwood07>Harwood, D.M., Nikolaev, V.A., and Winter, D.M. (2007). Cretaceous record of diatom evolution, radiation, and expansion. "Paleontological Society Papers" '''13''', 33–59</ref>
[[File:Diatoms-HCMR.jpg|thumb|250x250px|Diatoms ''Chaetoceros'' spp. on a membrane filter (pore size 0.4 μm) imaged using the Hellenic Centre for Marine Research scanning electron microscope. Thermaikos Gulf, Greece, 2004.]]
Although no mass extinctions of marine diatoms have been observed during the [[Cenozoic]], times of relatively rapid evolutionary turnover in marine diatom assemblages occurred near the [[Paleocene]]–[[Eocene]] boundary<ref name=Strelnikova90>Strelnikova, N. I. (1990). Evolution of diatoms during the Cretaceous and Paleogene periods. In: Simola, H. (ed.), "Proceedings of the Tenth International Diatom Symposium", Koeltz Scientific Books, Koenigstein, Germany, pp. 195–204</ref> and at the [[Eocene]]–[[Oligocene]] boundary.<ref name=Baldauf93>Baldauf, J.G. (1993). Middle Eocene through early Miocene diatom floral turnover. In: Prothero D., Berggren, W.H., (eds.), "Eocene-Oligocene climatic and biotic evolution", Princeton University Press, Princeton, NJ, USA, pp 310–326</ref>  Further turnover of assemblages took place at various times between the middle [[Miocene]] and late [[Pliocene]],<ref name=Barron03>Barron, J.A. (2003). Appearance and extinction of planktonic diatoms during the past 18 m.y. in the Pacific and Southern oceans. "Diatom Research" '''18''', 203–224</ref> 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]] to the [[Quaternary]].<ref name="Scherer07"/>  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]] expansion on [[Antarctica]] and progressive cooling through the [[Neogene]] and [[Quaternary]] towards a bipolar glaciated world. This drove the diatoms into uptaking silica more competitively (i.e., to use less silica in formation of their [[frustule]]s). 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]].

==Collection==
Living diatoms are often found clinging in great numbers to filamentous algae, or forming gelatinous masses on various submerged plants. ''[[Cladophora]]'' is frequently covered with ''[[Cocconeis]]'', an elliptically shaped diatom; ''Vaucheria'' is often covered with small forms. 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. They 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.

Since diatoms form an important part of the food of [[mollusc]]s, [[tunicate]]s, and [[fish]]es, the [[alimentary tract]]s of these animals often yield forms that are not easily secured in other ways. Marine diatoms can be collected by direct water sampling, though benthic forms can be secured by scraping [[barnacle]]s, [[oyster]] shells, and other shells.

This section uses text from ''Methods in Plant Histology''.<ref name=chamberlain1901>Chamberlain, C. J. (1901)  ''Methods in Plant Histology'', University of Chicago Press, USA</ref>

==Expressed sequence tagging==
The first insights into the properties of the ''[[Phaeodactylum tricornutum]]'' gene repertoire were described using 1,000 [[expressed sequence tag]]s (ESTs).<ref name=scala02>{{cite journal | last=Scala | first=S. | last2=Carels|first2= N.|last3= Falciatore|first3= A.|last4= Chiusano|first4= M.L.|last5= Bowler|first5= C. | title=Genome Properties of the Diatom Phaeodactylum tricornutum | journal=Plant Physiol. | volume=129 | issue=3 | pages=993–1002 |date=July 2002 | pmid=12114555 | pmc=166495 | doi=10.1104/pp.010713 | url=http://www.plantphysiol.org/cgi/content/full/129/3/993 }}</ref> Subsequently, the number of ESTs was extended to 12,000 and the diatom EST database was constructed for functional analyses.<ref name=maheswari05>{{cite journal | last1 = Maheswari | first1 = U. | last2 = Montsant | first2 = A. | last3 = Goll | first3 = J. | last4 = Krishnasamy | first4 = S. | last5 = Rajyashri | first5 = K.R. | last6 = Patell | first6 = V.M. | last7 = Bowler | first7 = C. | year = 2005 | title = The Diatom EST Database | url = http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D344 | journal = Nucleic Acids Research | volume = 33 | issue = Database issue| pages = 344–347 | pmid = 15608213 | doi = 10.1093/nar/gki121 | pmc = 540075 }}</ref> These sequences have been used to make a comparative analysis between ''P. tricornutum'' and the putative complete proteomes from the [[green algae|green alga]] ''[[Chlamydomonas reinhardtii]]'', the [[red alga]] ''[[Cyanidioschyzon merolae]]'', and the diatom ''[[Thalassiosira pseudonana]]''.<ref name=montsant05>{{cite journal | last=Montsant |first=A. | last2=Jabbari|first2= K.|last3= Maheswari|first3= U. |last4= Bowler|first4= C. | title=Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum | journal=Plant Physiol. | volume=137 | issue=2 | pages=500–13 |date=February 2005 | pmid=15665249 | pmc=1065351 | doi=10.1104/pp.104.052829 }}</ref> 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 (available at http://www.biologie.ens.fr/diatomics/EST3/).<ref>Maheswari U, Mock T, Armbrust EV, Bowler C: Update of the Diatom EST Database: a new tool for digital transcriptomics. Nucleic Acids Res 2008.</ref>

==Genome sequencing==
The entire [[genome]]s of the centric diatom, ''[[Thalassiosira pseudonana]]'' (32.4 Mb),<ref name=armbrust04>{{cite journal | last1 = Armbrust | first1 =   E. V.| year = 2004 | title = The genome of the diatom ''Thalassiosira pseudonana'': ecology, evolution, and metabolism | url = http://www.sciencemag.org/cgi/content/abstract/306/5693/79 | journal = Science | volume = 306 | issue = 5693| pages = 79–86 | doi=10.1126/science.1101156 | pmid=15459382|bibcode = 2004Sci...306...79A | last2 = Berges | first2 = JA | last3 = Bowler | first3 = C | last4 = Green | first4 = BR | last5 = Martinez | first5 = D | last6 = Putnam | first6 = NH | last7 = Zhou | first7 = S | last8 = Allen | first8 = AE | last9 = Apt | first9 = KE | last10 = Bechner | first10 = M | last11 = Brzezinski | first11 = MA | last12 = Chaal | first12 = BK | last13 = Chiovitti | first13 = A | last14 = Davis | first14 = AK | last15 = Demarest | first15 = MS | last16 = Detter | first16 = JC | last17 = Glavina | first17 = T | last18 = Goodstein | first18 = D | last19 = Hadi | first19 = MZ | last20 = Hellsten | first20 = U | last21 = Hildebrand | first21 = M | last22 = Jenkins | first22 = BD | last23 = Jurka | first23 = J | last24 = Kapitonov | first24 = VV | last25 = Kröger | first25 = N | last26 = Lau | first26 = WW | last27 = Lane | first27 = TW | last28 = Larimer | first28 = FW | last29 = Lippmeier | first29 = JC | last30 = Lucas | first30 = S }}</ref> and the pennate diatom, ''[[Phaeodactylum tricornutum]]'' (27.4 Mb),<ref name=bowler08>{{cite journal | last=Bowler | first=C. | year=2008 | title=The Phaeodactylum genome reveals the evolutionary history of diatom genomes | journal=[[Nature (journal)|Nature]] | volume=456 | pages=239–244 | doi=10.1038/nature07410 | pmid=18923393 | issue=7219 |bibcode = 2008Natur.456..239B | last3=Badger | first3=J. H. | last4=Grimwood | first4=J | last5=Jabbari | first5=K | last6=Kuo | first6=A | last7=Maheswari | first7=U | last8=Martens | first8=C | last9=Maumus | first9=F | last10=Otillar | first10=R. P. | last11=Rayko | first11=E | last12=Salamov | first12=A | last13=Vandepoele | first13=K | last14=Beszteri | first14=B | last15=Gruber | first15=A | last16=Heijde | first16=M | last17=Katinka | first17=M | last18=Mock | first18=T | last19=Valentin | first19=K | last20=Verret | first20=F | last21=Berges | first21=J. A. | last22=Brownlee | first22=C | last23=Cadoret | first23=J. P. | last24=Chiovitti | first24=A | last25=Choi | first25=C. J. | last26=Coesel | first26=S | last27=De Martino | first27=A | last28=Detter | first28=J. C. | last29=Durkin | first29=C | last30=Falciatore | first30=A |display-authors=etal}}</ref> have been [[genome sequencing|sequenced]]. Comparisons of the two fully sequenced diatom genomes finds that the ''P. tricornutum'' genome includes fewer genes (10,402 opposed to 11,776) than ''T. pseudonana'' and 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.<ref name=bowler08/><ref>{{cite journal | last1 = Roy | first1 = SW | last2 = Penny | first2 = D | date = Jul 2007 | title = A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain | url = | journal = Mol Biol Evol. | volume = 24 | issue = 7| pages = 1447–57 | doi = 10.1093/molbev/msm048 | pmid = 17350938 }}</ref> Despite relatively recent evolutionary divergence (90 million years), the extent of molecular divergence between centrics and pennates indicates rapid evolutionary rates within the Bacillariophyceae compared to other eukaryotic groups.<ref name=bowler08/> Comparative genomics also established that a specific class of [[transposable elements]], 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.<ref name=maumus09>{{cite journal | last=Maumus |first=F. |author2=Allen, A.E.|author3=Mhiri, C.|author4=Hu, H.|author5=Jabbari, K.|author6=Vardi, A.|author7=Grandbastien, M.A.|author8=Bowler, C. | title=Potential impact of stress activated retrotransposons on genome evolution in a marine diatom | journal=BMC Genomics | year=2009 | pmid=20028555 | pmc=2806351 | doi=10.1186/1471-2164-10-624 | volume=10 | pages=624}} {{open access}}</ref>

Importantly, diatom genomics brought much information about the extent and dynamics of the endosymbiotic gene transfer (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]]) [[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.<ref name="armbrust04"/> More recent phylogenomic analyses of diatom proteomes provided evidence for a prasinophyte-like endosymbiont in the common ancestor of [[chromalveolates]] 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]]s. Therefore, it was proposed that chromalveolates are the product of serial secondary endosymbiosis first with a green algae, followed by a second one with a red algae that conserved the genomic footprints of the previous but displaced the green plastid.<ref>{{cite journal | last1 = Moustafa | first1 = A | last2 = Beszteri | first2 = B | last3 = Maier | first3 = UG | last4 = Bowler | first4 = C | last5 = Valentin | first5 = K | last6 = Bhattacharya | first6 = D | year = 2009 | title = Genomic footprints of a cryptic plastid endosymbiosis in diatoms | url = | journal = Science | volume = 324 | issue = | pages = 1724–1726 | doi=10.1126/science.1172983|bibcode = 2009Sci...324.1724M | pmid=19556510}}</ref> 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.

In addition to EGT, [[horizontal gene transfer]] (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.<ref name="bowler08"/>

==Forensic research==
The main goal of diatom analysis in [[forensic]]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]] of drowning as the [[cause of death]]. Further matching of [[diatoms]] from bone marrow and drowning site can strengthen this supportive evidence and a positive conclusion can be drawn whether a person was living or not when submerged.<ref>{{cite journal |last1=Verma |first1=K. |year=2013 |title=Role of Diatoms in the World of Forensic Science |journal=J. Forensic. Res. |volume=4 |issue= 2|pages= |publisher= |doi=10.4172/2157-7145.1000181 |url=http://www.omicsonline.org/2157-7145/2157-7145-4-181.php?aid=14679 |accessdate=5 September 2013}}</ref>

==Nanotechnology research==
The deposition of silica by diatoms may also prove to be of utility to [[nanotechnology]].<ref name=bradbury04>{{cite journal | last1 = Bradbury | first1 = J. | year = 2004 | title = Nature's Nanotechnologists: Unveiling the Secrets of Diatoms | journal = PLoS Biology | volume = 2 | issue = 10| pages = 1512–1515 | doi = 10.1371/journal.pbio.0020306 | pmid=15486572 | pmc=521728}} {{open access}}</ref> 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]] [[nanolithography]]; and even using diatom valves as vehicles for [[drug delivery]]. Using an appropriate [[artificial selection|artificial selection procedure]], diatoms that produce valves of particular shapes and sizes could be evolved in the laboratory, and then used in [[chemostat]] cultures to [[mass production|mass-produce]] nanoscale components.<ref name=drum03>{{cite journal | last=Drum | first=R.W. |author2=Gordon, R. | year=2003 | title=Star Trek replicators and diatom nanotechnology | journal=Trends Biotechnology | volume=21 | pages=325–328 | doi=10.1016/S0167-7799(03)00169-0 | url=http://www.cell.com/trends/biotechnology/abstract/S0167-7799(03)00169-0?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0167779903001690%3Fshowall%3Dtrue&cc=y=}}</ref> It has also been proposed that diatoms could be used as a component of solar cells, by substituting [[Photosensitivity|photosensitive]] [[titanium dioxide]] for the silicon dioxide normally used in the creation of cell walls.<ref>{{cite web | url=http://www.eetimes.com/showArticle.jhtml?articleID=216500176 | title=Diatoms could triple solar cell efficiency | last=Johnson | first=R.C. | date=9 April 2009 | accessdate=13 April 2009 | publisher=[[EE Times]] }}</ref> Diatom biofuel producing solar panels have also been proposed.<ref>Ramachandra, T.V., D.M. Mahapatra, Karthick B. & R. Gordon [http://pubs.acs.org/doi/abs/10.1021/ie900044j Milking diatoms for sustainable energy: biochemical engineering versus gasoline-secreting diatom solar panels] Industrial & Engineering Chemistry Research 48(19, Complex Materials II special issue, October), 8769-8788 2009</ref>

== Microbial degradation ==

Certain species of bacteria in oceans and lakes can accelerate the rate of dissolution of silica in dead and living diatoms by using [[hydrolytic]] enzymes to break down the organic algal material.<ref>{{cite journal|url=http://www.nature.com/nature/journal/v397/n6719/abs/397508a0.html|title=Accelerated dissolution of diatom silica by marine bacterial assemblages|author1=Kay D. Bidle|author2=Farooq Azam|journal=Nature|year=1999|volume=397|pages=508–512|issue=6719|doi=10.1038/17351|bibcode = 1999Natur.397..508B }}</ref><ref>{{cite journal|url=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059977|title=The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal|year=2013 | doi=10.1371/journal.pone.0059977|volume=8|journal=PLoS ONE|pages=e59977|bibcode = 2013PLoSO...859977Z }} {{open access}}</ref>

==See also==
* [[Algae]]
* [[Biological pump]]
* [[Diatomaceous earth]]
* [[Phytoplankton]]
* [[Plankton]]

==References==
{{reflist|2}}

==External links==
{{wikispecies | Bacillariophyta | Diatoms}}
{{Commons category|Diatoms}}
* [http://research.calacademy.org/research/diatoms/names/ Catalogue of Diatom Names, California Academy of Sciences]
* [http://genome.jgi-psf.org/Thaps3/Thaps3.home.html Diatom Genome], [[Joint Genome Institute]]
* [http://www.biologie.ens.fr/diatomics/EST/ Diatom EST database], [[École Normale Supérieure]]
* [http://planktonnet.awi.de Plankton*Net], [[Taxonomy (biology)|taxonomic]] database including images of diatom species
* [http://www.ucmp.berkeley.edu/chromista/diatoms/diatomlh.html Life History and Ecology of Diatoms], [[University of California Museum of Paleontology]]
* [http://cabinetoffreshwatercuriosities.com/2012/03/20/diatoms-a-freshwater-curiosity/ Diatoms: A Freshwater Curiosity], The BioFresh Cabinet of Freshwater Curiosities
* [http://hjs.geol.uib.no/Diatoms/index.html-ssi Diatoms: 'Nature's Marbles'], Eureka site, [[University of Bergen]]
* [http://www.ucl.ac.uk/GeolSci/micropal/diatom.html Diatom life history and ecology], Microfossil Image Recovery and Circulation for Learning and Education (MIRACLE), [[University College London]]
* [http://www.rbge.org.uk/science/cryptogamic-plants-and-fungi/phycology/diatoms Diatom page], [[Royal Botanic Garden Edinburgh]]
* [http://www.microscopy-uk.org.uk/mag/artfeb05/cbdiatoms.html Geometry and Pattern in Nature 3: The holes in radiolarian and diatom tests]
* [http://www1.tip.nl/%7Et936927/art_deco.html Art Deco Diatoms], Wim van Egmond
* [http://www.mbari.org/staff/conn/botany/phytoplankton/phytoplankton_diatoms.htm Diatom QuickFacts], [[Monterey Bay Aquarium Research Institute]]
* [http://diatom.ansp.org/algae_image/ Algae image database] [[Academy of Natural Sciences of Philadelphia]] (ANSP)
* [http://diatom.ansp.org/nawqa/Taxalist.aspx Diatom taxa] [[Academy of Natural Sciences of Philadelphia]] (ANSP)
* [http://www.deccanherald.com/content/20100/now-energy-single-celled-algae.html/ Now, energy from single celled algae] ''[[Deccan Herald]]''
* [http://pubs.acs.org/cgi-bin/abstract.cgi/langd5/asap/abs/la702278f.html Computer simulations of pattern formation in diatoms]
* [http://www.mrkism.com/diatomea/ aDiatomea, an artificial life experiment with highly detailed 3d generated diatoms]
*[http://www.cmog.org/article/glass-nature Glass in Nature, The Corning Museum of Glass]

{{plankton}}
{{Chromalveolata}}
{{Use dmy dates|date=August 2011}}

{{Authority control}}

[[Category:Algae classes]]
[[Category:Biological oceanography]]
[[Category:Diatoms|*]]
[[Category:Planktology]]