View source for Diatom

{{short description|Single-celled alga with a silica cell wall}}
{{for|a molecule of two atoms|Diatomic molecule}}
{{Use dmy dates|date=December 2019}}
{{Automatic taxobox
| fossil_range = {{fossilrange|Jurassic|Present}}
| image = Diatoms through the microscope.jpg
| image_upright = 1.2
| image_caption = Light microscopy of a sampling of marine diatoms found living between crystals of annual sea ice in Antarctica, showing a multiplicity of sizes and shapes
| display_parents = 2
| taxon = Diatomeae
| authority = [[Barthélemy Charles Joseph Dumortier|Dumortier]], 1821<ref>{{cite book |last=Dumortier |first=B.-C. |year=1822 |url=http://images.algaebase.org/pdf/AC100CF013cd51B91ERyQ180397B/16499.pdf |title=Commentationes botanicae. Observations botaniques, dédiées à la Société d'Horticulture de Tournay |archive-url=https://web.archive.org/web/20151006091814/http://images.algaebase.org/pdf/AC100CF013cd51B91ERyQ180397B/16499.pdf |archive-date=6 October 2015 |via=Algaebase |pages=[i], [1]-116, [1, tabl., err.] |location=Tournay |publisher=Imprimerie de Ch. Casterman-Dieu, Rue de pont No. 10}}</ref><ref name="Adl-2018"/>
| subdivision_ranks = Subgroups<ref name="Adl-2018">{{Cite journal |last1=Adl |first1=Sina M. |last2=Bass |first2=David |last3=Lane|first3=Christopher E. |last4=Lukeš |first4=Julius |last5=Schoch |first5=Conrad L. |last6=Smirnov |first6=Alexey |last7=Agatha |first7=Sabine |last8=Berney |first8=Cedric |last9=Brown |first9=Matthew W. | display-authors = 6 | date=2018-09-26 |title=Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes|journal=Journal of Eukaryotic Microbiology |volume=66 |issue=1 |pages=4–119 |doi=10.1111/jeu.12691|pmid=30257078 |pmc=6492006 }}</ref>
| subdivision = *[[Leptocylindrophytina]]
**[[Leptocylindrophyceae]]
**[[Corethrophyceae]]
*[[Ellerbeckia|Ellerbeckiophytina]]
*[[Probosciophytina]]
*[[Melosirophytina]]
*[[Coscinodiscophytina]]
*[[Rhizosoleniophytina]]
*[[Arachnoidiscophytina]]
*[[Bacillariophytina]]
**[[Mediophyceae]]
***[[Chaetocerotophycidae]]
***[[Lithodesmiophycidae]]
***[[Thalassiosirophycidae]]
***[[Cymatosirophycidae]]
***[[Odontellophycidae]]
***[[Chrysanthemodiscophycidae]]
**[[Biddulphiophyceae]]
***[[Biddulphiophycidae]]
***''[[Attheya]]''
**[[Bacillariophyceae]]
***[[Urneidophycidae]]
***[[Fragilariophycidae]]
***[[Bacillariophycidae]]
***[[Striatellaceae]]
| synonyms = * [[Bacillariophyceae]] {{au|[[Pierre Dangeard|Dangeard]], 1933}}<ref>Dangeard, P. (1933). ''Traite d'Algologie.'' Paul Lechvalier and Fils, Paris, [https://books.google.com/books?id=mDxVAAAAMAAJ] {{Webarchive|url=https://web.archive.org/web/20151004183804/https://books.google.com/books?id=mDxVAAAAMAAJ |date=4 October 2015 }}.</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] {{Webarchive|url=https://web.archive.org/web/20141110205527/http://caliban.mpipz.mpg.de/haeckel/protistenreich/high/IMG_8499.html |date=10 November 2014 }}.''</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>
}}

A '''diatom''' ([[Neo-Latin]] ''diatoma''){{efn|From {{langx|el|διατομή|diatomé}}, "a cutting through, a severance",<ref name="lsjdiatome">{{LSJ|diatomh/|διατομή|ref}}</ref> from {{langx|el|διάτομος|diátomos}}, "cut in half, divided equally" <ref name="lsjdiatomos">{{LSJ|dia/tomos|διάτομος|ref}}</ref> from {{langx|el|διατέμνω| diatémno}}, "to cut in twain".<ref name="lsjdiatemnw">{{LSJ|dia/temnw|διατέμνω|ref}}</ref><ref name="Clarendon Press-1971">{{Cite encyclopedia |title=The Compact Oxford English Dictionary |year=1971 |publisher=Clarendon Press |isbn=0-918414-08-3}}</ref>{{rp|718}}}} is any member of a large group comprising several [[Genus|genera]] of [[algae]], specifically [[microalgae]], found in the oceans, waterways and soils of the world. Living diatoms make up a significant portion of Earth's [[Biomass (ecology)|biomass]]. They generate about 20 to 50 percent of the [[oxygen]] produced on the planet each year,<ref>{{cite web |url=https://www.livescience.com/46250-teasing-apart-the-diatom-genome.html |title=The Air You're Breathing? A Diatom Made That |website=[[Live Science]] |date=11 June 2014 |access-date=30 April 2018 |archive-date=30 April 2018 |archive-url=https://web.archive.org/web/20180430115059/https://www.livescience.com/46250-teasing-apart-the-diatom-genome.html |url-status=live}}</ref><ref>{{Cite web |url=https://diatoms.org/what-are-diatoms |title=What are Diatoms? |publisher=Diatoms of North America |access-date=28 January 2020 |archive-url=https://web.archive.org/web/20200125061107/https://diatoms.org/what-are-diatoms |archive-date=25 January 2020 }}</ref> take in over 6.7 billion tonnes of [[silicon]] each year from the waters in which they live,<ref>{{cite journal | last1=Treguer | first1=P. | last2=Nelson | first2=D. M. | last3=Van Bennekom | first3=A. J. | last4=Demaster | first4=D. J. | last5=Leynaert | first5=A. | last6=Queguiner | first6=B. | year=1995 | title=The Silica Balance in the World Ocean: A Reestimate | bibcode=1995Sci...268..375T | journal=Science | volume=268 | issue=5209| pages=375–9 | doi=10.1126/science.268.5209.375 | pmid=17746543 | s2cid=5672525 }}</ref> and constitute nearly half of the organic material found in the oceans. The [[Protist shell|shells]] of dead diatoms are a significant component of [[marine sediment]], and the entire [[Amazon basin]] is fertilized annually by 27 million tons of [[diatomaceous earth|diatom shell dust]] transported by transatlantic winds from the African [[Sahara]], much of it from the [[Bodélé Depression]], which was once made up of a system of fresh-water lakes.<ref>{{Cite web|url=https://www.kcl.ac.uk/sspp/departments/geography/people/academic/drake/Research/The-Sahara-Megalakes-Project/Lake-Megachad.aspx|title=King's College London – Lake Megachad|website=www.kcl.ac.uk|language=en-GB|access-date=5 May 2018|archive-date=27 November 2018|archive-url=https://web.archive.org/web/20181127124138/https://www.kcl.ac.uk/sspp/departments/geography/people/academic/drake/Research/The-Sahara-Megalakes-Project/Lake-Megachad.aspx|url-status=live}}</ref><ref>{{cite journal |last1=Bristow |first1=C.S. |author2-link=Karen Hudson-Edwards |last2=Hudson-Edwards |first2=K.A. |last3=Chappell |first3=A. |date=2010 |title=Fertilizing the Amazon and equatorial Atlantic with West African dust |journal=Geophys. Res. Lett. |volume=37 |issue=14|pages=L14807 |doi=10.1029/2010GL043486 |bibcode=2010GeoRL..3714807B |s2cid=128466273 }}</ref>

Diatoms are [[unicellular organism]]s: they occur either as solitary cells or in [[Colony (biology)|colonies]], which can take the shape of ribbons, fans, zigzags, or stars. Individual cells range in size from 2 to 2000 micrometers.<ref name="Hasle-1996" /> In the presence of adequate nutrients and sunlight, an assemblage of living diatoms doubles approximately every 24 hours by [[asexual reproduction|asexual]] [[Fission (biology)#Multiple fission|multiple fission]]; the maximum life span of individual cells is about six days.<ref>{{Cite web | url=https://www.smithsonianmag.com/science-nature/gas-guzzlers-1-106582382/ | title=Gas Guzzlers | access-date=22 May 2018 | archive-date=22 May 2018 | archive-url=https://web.archive.org/web/20180522181520/https://www.smithsonianmag.com/science-nature/gas-guzzlers-1-106582382/ | url-status=live }}</ref> Diatoms have two distinct shapes: a few (''centric diatoms'') are ''radially'' symmetric, while most (''pennate diatoms'') are broadly ''bilaterally'' symmetric.

About 12,000 species of diatoms have been documented, but it is thought many more have not been documented. The unique feature of diatoms is that they are surrounded by 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 | access-date=20 May 2015 | archive-url=https://web.archive.org/web/20121004130024/http://www.ucmp.berkeley.edu/chromista/diatoms/diatommm.html | archive-date=4 October 2012 }}</ref> These frustules produce [[structural coloration]], 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]]s and wind-induced water [[turbulence]]; however, male [[gamete]]s of centric diatoms have [[flagellum|flagella]], permitting active movement to seek female gametes. Similar to [[plant]]s, diatoms convert [[light|light energy]] to [[chemical energy]] by [[photosynthesis]], but their chloroplasts were acquired in different ways.<ref name="van den Hoek-1995">{{cite book |title=Algae: an introduction to Phycology |last1=van den Hoek |first1=C. |last2=Mann |first2=D.G. |last3=Jahns |first3=H.M. |publisher=[[Cambridge University Press]] |year=1995 |isbn=978-0-521-31687-3 |location=Cambridge |pages=165–218}}</ref>

Unusually for autotrophic organisms, diatoms possess a [[urea cycle]], a feature that they share with [[animal]]s, although this cycle is used to different metabolic ends in diatoms. The family [[Rhopalodiaceae]] also possess a [[cyanobacteria]]l [[endosymbiont]] called a spheroid body. This endosymbiont has lost its photosynthetic properties, but has kept its ability to perform [[nitrogen fixation]], allowing the diatom to fix atmospheric nitrogen.<ref>{{Cite journal |pmc=4128115 |year=2014 |last1=Nakayama |first1=T. |title=Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=111 |issue=31 |pages=11407–11412 |last2=Kamikawa |first2=R. |last3=Tanifuji |first3=G. |last4=Kashiyama |first4=Y. |last5=Ohkouchi |first5=N. |last6=Archibald |first6=J. M. |last7=Inagaki |first7=Y. |pmid=25049384 |doi=10.1073/pnas.1405222111 |bibcode=2014PNAS..11111407N |doi-access=free}}</ref> Other diatoms in symbiosis with nitrogen-fixing cyanobacteria are among the genera ''[[Hemiaulus]]'', ''[[Rhizosolenia]]'' and ''[[Chaetoceros]]''.<ref>{{Cite journal |last1=Pierella Karlusich |first1=Juan José |last2=Pelletier |first2=Eric |last3=Lombard |first3=Fabien |last4=Carsique |first4=Madeline |last5=Dvorak |first5=Etienne |last6=Colin |first6=Sébastien |last7=Picheral |first7=Marc |last8=Cornejo-Castillo |first8=Francisco M. |last9=Acinas |first9=Silvia G. |last10=Pepperkok |first10=Rainer |last11=Karsenti |first11=Eric |date=2021-07-06 |title=Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods |journal=Nature Communications |language=en |volume=12 |issue=1 |page=4160 |doi=10.1038/s41467-021-24299-y |issn=2041-1723 |pmc=8260585 |pmid=34230473 |bibcode=2021NatCo..12.4160P}}</ref>

Dinotoms are diatoms that have become endosymbionts inside [[dinoflagellates]]. Research on the dinoflagellates ''Durinskia baltica'' and ''[[Glenodinium foliaceum]]'' has shown that the endosymbiont event happened so recently, evolutionarily speaking, that their organelles and genome are still intact with minimal 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.<ref>[https://academic.oup.com/mbe/article/33/9/2376/2579291?login=false Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont | Molecular Biology and Evolution | Oxford Academic]</ref>

The study of diatoms is a branch of [[phycology]]. Diatoms are classified as [[eukaryote]]s, organisms with a [[nuclear envelope]]-bound [[cell nucleus]], that separates them from the [[prokaryote]]s [[archaea]] and [[bacteria]]. Diatoms are a type of [[plankton]] called [[phytoplankton]], the most common of the plankton types. Diatoms also grow attached to [[benthic zone|benthic]] substrates, floating debris, and on [[aquatic plant|macrophyte]]s. They comprise an integral component of the [[periphyton]] community.<ref>{{cite book |editor-last=Wehr |editor-first=J. D. |editor2-last=Sheath |editor2-first=R. G. |editor3-last=Kociolek |editor3-first=J. P. |year=2015 |title=Freshwater Algae of North America: Ecology and Classification |edition=2nd |location=San Diego |publisher=Academic Press |isbn=978-0-12-385876-4 }}</ref> 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]] exist.

[[Fossil]] evidence suggests that diatoms originated during or before the early [[Jurassic]] 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.<ref>{{Cite journal|last1=Girard|first1=Vincent|last2=Saint Martin|first2=Simona|last3=Buffetaut|first3=Eric|last4=Saint Martin|first4=Jean-Paul|last5=Néraudeau|first5=Didier|last6=Peyrot|first6=Daniel|last7=Roghi|first7=Guido|last8=Ragazzi|first8=Eugenio|last9=Suteethorn|first9=Varavudh|date=2020|title=Thai amber: insights into early diatom history?|journal=BSGF - Earth Sciences Bulletin|volume=191|page=23|doi=10.1051/bsgf/2020028|issn=1777-5817|doi-access=free|hdl=11577/3391076|hdl-access=free}}</ref>

Diatoms are used to monitor past and present environmental conditions, and are commonly used in studies of water quality. [[Diatomaceous earth]] (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.

[[File:Dwindling diatoms and the mixed layer.ogg|thumb|upright=1.9| {{center|'''Dwindling diatoms and the mixed layer'''}} Earth's oceans teem with microscopic plants called [[phytoplankton]]. But according to a 2015 NASA study, populations of diatoms, the largest type of phytoplankton algae, have declined more than 1 percent per year from 1998 to 2012. Phytoplankton are an essential base of the [[marine food web]] and absorb carbon dioxide dissolved in the ocean that originally came from the atmosphere. The tiny organisms occupy the uppermost layer of ocean water, called the [[mixed layer]], where waves and currents continually churn, drawing up nutrients from a deeper layer of water below. Scientists say the phytoplankton declines observed over the 15-year study period are due to the mixed layer becoming shallower, which results in fewer nutrients reaching the diatoms. The reduction in population may reduce the amount of carbon dioxide drawn out of the atmosphere and transferred to the deep ocean for long-term storage.<ref name="NASA-2018">[https://blogs.nasa.gov/earthexpeditions/2018/09/04/the-inner-space-of-the-subarctic-pacific-ocean/ The Inner Space of the Subarctic Pacific Ocean] {{Webarchive|url=https://web.archive.org/web/20201027125701/https://blogs.nasa.gov/earthexpeditions/2018/09/04/the-inner-space-of-the-subarctic-pacific-ocean/ |date=27 October 2020 }} ''NASA Earth Expeditions'', 4 September 2018. {{PD-notice}}</ref><ref>{{cite journal |doi=10.1002/2015GB005139 |title=Recent decadal trends in global phytoplankton composition |year=2015 |last1=Rousseaux |first1=Cecile S. |last2=Gregg |first2=Watson W. |journal=Global Biogeochemical Cycles |volume=29 |issue=10 |pages=1674–1688 |bibcode=2015GBioC..29.1674R |doi-access=free}}</ref>]]

==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.<ref>{{cite journal | last1=Nelson | first1=David M. | last2=Tréguer | first2=Paul | last3=Brzezinski | first3=Mark A. | last4=Leynaert | first4=Aude | last5=Quéguiner | first5=Bernard | title=Production and dissolution of biogenic silica in the ocean: Revised global estimates, comparison with regional data and relationship to biogenic sedimentation | journal=Global Biogeochemical Cycles | publisher=American Geophysical Union (AGU) | volume=9 | issue=3 | year=1995 | issn=0886-6236 | doi=10.1029/95gb01070 | pages=359–372| bibcode=1995GBioC...9..359N }}</ref> 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{{hsp}}<ref>{{cite journal | last=Mann | first=David G. | title=The species concept in diatoms | journal=Phycologia | publisher=Informa UK Limited | volume=38 | issue=6 | year=1999 | issn=0031-8884 | doi=10.2216/i0031-8884-38-6-437.1 | pages=437–495| bibcode=1999Phyco..38..437M }}</ref> that are distributed between the two major diatom groups: centrics and pennates.<ref>Simonsen, R., (1979). "The diatom system: ideas on phylogeny", ''Bacillaria'', '''2''': 9–71.</ref><ref name="Moore-2017">{{cite journal | last1=Moore | first1=Eric R. | last2=Bullington | first2=Briana S. | last3=Weisberg | first3=Alexandra J. | last4=Jiang | first4=Yuan | last5=Chang | first5=Jeff | last6=Halsey | first6=Kimberly H. | title=Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms | journal=PLOS ONE | publisher=Public Library of Science (PLoS) | volume=12 | issue=7 | date=2017-07-07 | issn=1932-6203 | doi=10.1371/journal.pone.0181098 | article-number=e0181098| pmid=28686696 | pmc=5501676 | bibcode=2017PLoSO..1281098M | doi-access=free }} [[File:CC-BY icon.svg|50px]] Modified material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>

==Morphology==
[[File:2023 Diatom.svg|thumb|upright=1.9|{{center|'''Representation of a diatom'''}} {{ordered list| Central nodule|Striae; pores, punctae, spots or dots in a line on the surface that allow nutrients in, and waste out, of the cell |
[[Areolae (diatom)|Areola]]; hexagonal or polygonal boxlike perforation with a sieve present on the surface of diatom |[[Raphe]]; slit in the valves  |Polar nodule; thickening of wall at the distal ends of the raphe <ref>Taylor, J. C., Harding, W. R. and Archibald, C. (2007). ''An Illustrated Guide to Some Common Diatom Species from South Africa''. Gezina: Water Research Commission. {{ISBN|9781770054844}}.</ref><ref>Mishra, M., Arukha, A.P., Bashir, T., Yadav, D. and Prasad, G.B.K.S. (2017) "All new faces of diatoms: potential source of nanomaterials and beyond". ''Frontiers in microbiology'', '''8''': 1239. {{doi|10.3389/fmicb.2017.01239|doi-access=free}}. [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=16 October 2017 }}.</ref>|[[Frustule]]; hard and porous cell wall |[[Pyrenoid]]; center of [[carbon fixation]] |[[Plastid]] membranes (4, secondary red) |Inner membranes |[[Thylakoid]]; site of the [[light-dependent reactions]] of [[photosynthesis]] |[[Oil body]]; storage for triacylglycerols <ref>{{cite journal|journal=Philosophical Transactions of the Royal Society B|last=Maeda|first=Yoshiaki|title=Structure and properties of oil bodies in diatoms|date=2017-07-17|volume=372|issue=1728|doi=10.1098/rstb.2016.0408 |pmid=28717018 |pmc=5516117 }}</ref>|[[Mitochondria|Mitochondrion]]; creates [[Adenosine triphosphate|ATP]] (energy) for the cell |[[Vacuole]]s; vesicle of a cell that contains fluid bound by a membrane |Cytoplasmic strand; holds the nucleus |Protoplasmic bridge| Epivalve|[[Cell nucleus|Nucleus]]; holds the genetic material |[[Endoplasmic reticulum]], the transport network for molecules going to specific parts of the cell||[[Golgi apparatus]]; modifies [[protein]]s and sends them out of the cell |Epicingulum|Hypocingulum|Hypovalve|[[Microtubule]] centre}}]]

[[File:3D-animation of the diatom Corethron sp.ogg|thumb|upright=1.8| {{center|'''3D-animation of the diatom ''Corethron'' sp.'''<br />Displays overlays from four fluorescent channels}}(a) Green: [DiOC6(3) fluorescence] - stains cellular membranes indicating the core cell bodies<br />(b) Cyan: [PLL-A546 fluorescence] - generic counterstain for visualising eukaryotic cell surfaces<br />(c) Blue: [Hoechst fluorescence] - stains DNA, identifies nuclei<br />(d) Red: [chlorophyll autofluorescence] - resolves chloroplasts{{hsp}}<ref name="Colin-2017">Colin, S., Coelho, L.P., Sunagawa, S., Bowler, C., Karsenti, E., Bork, P., Pepperkok, R. and De Vargas, C. (2017) "Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes". ''eLife'', '''6''': e26066. {{doi|10.7554/eLife.26066.002|doi-access=free}}. [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=16 October 2017 }}.</ref><br /><small> {{center|The animation starts by overlaying all available fluorescent channels, and then clarifies the visualisation by switching channels on and off}}</small>]]Diatoms are generally 20 to 200 micrometers in size,<ref>University College London (2002) [https://www.ucl.ac.uk/GeolSci/micropal/diatom.html#:~:text=Diatoms%20are%20commonly%20between%2020,by%20bands%20into%20long%20chains). Diatoms] {{Webarchive|url=https://web.archive.org/web/20110927231912/http://www.ucl.ac.uk/GeolSci/micropal/diatom.html#:~:text=Diatoms%20are%20commonly%20between%2020,by%20bands%20into%20long%20chains). |date=27 September 2011 }} ''Micropalaeontology Unit''.</ref> with a few larger species. Their yellowish-brown [[chloroplast]]s, the site of photosynthesis, are typical of [[heterokont]]s, having four [[cell membrane]]s 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, including the hairs ([[mastigoneme]]s) characteristic in other groups.

Diatoms are often referred as "jewels of the sea" or "living opals" due to their optical properties.<ref>{{cite journal |doi=10.1038/nnano.2007.152 |pmid=18654305 |title=Biomimetics of photonic nanostructures |journal=Nature Nanotechnology |volume=2 |issue=6 |pages=347–53 |year=2007 |last1=Parker |first1=Andrew R. |last2=Townley |first2=Helen E. |bibcode=2007NatNa...2..347P }}</ref> The biological function of this [[structural coloration]] is not clear, but it is speculated that it may be related to communication, camouflage, thermal exchange and/or UV protection.<ref>{{cite journal |doi=10.1016/j.tibtech.2008.11.003 |pmid=19167770 |title=The Glass Menagerie: Diatoms for novel applications in nanotechnology |journal=Trends in Biotechnology |volume=27 |issue=2 |pages=116–27 |year=2009 |last1=Gordon |first1=Richard |last2=Losic |first2=Dusan |last3=Tiffany |first3=Mary Ann |last4=Nagy |first4=Stephen S. |last5=Sterrenburg |first5=Frithjof A.S. }}</ref>

Diatoms build intricate hard but porous cell walls called [[frustule]]s composed primarily of [[silica]].<ref name="Rita A. Horner-2002" />{{rp|25–30}} This siliceous wall<ref name="CMOG-2013">{{cite web|title=Glass in Nature|url=http://www.cmog.org/article/glass-nature|publisher=The Corning Museum of Glass|access-date=19 February 2013|archive-url=https://web.archive.org/web/20130307120741/http://www.cmog.org/article/glass-nature|archive-date=7 March 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 ''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]]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.

[[File:Diatomeas-Haeckel.jpg|thumb|upright=1.3|left|Selections from [[Ernst Haeckel]]'s 1904 {{lang|de|[[Kunstformen der Natur]]}} (''Art Forms of Nature''), showing pennate (left) and centric (right) frustules.]]
[[File:Shape classification of diatom frustules.png|thumb|upright=1.3|left| {{center|Shape classification of diatom frustules. The images are 3D models. The actual sizes of the frustules are about 10–80&nbsp;μm.<ref name="Zhang-2012" />}}]]
[[File:Structure of diatom frustules.png|thumb|upright=1.3|right|{{center|Structure of a centric diatom frustule <ref name="Zhang-2012">{{cite journal|last1=Zhang|first1=D.|last2=Wang|first2=Y.|last3=Cai|first3=J.|last4=Pan|first4=J.|last5=Jiang|first5=X.|last6=Jiang|first6=Y.|year=2012|title=Bio-manufacturing technology based on diatom micro- and nanostructure|journal=Chinese Science Bulletin|volume=57|issue=30|pages=3836–3849|doi=10.1007/s11434-012-5410-x|bibcode=2012ChSBu..57.3836Z|doi-access=free}}</ref>}}]]
{{clear}}

==Silicification==
{{see also|Silicification}}

Diatom cells are contained within a unique silica [[cell wall]] known as a [[frustule]] made up of two valves called [[theca]]e, that typically overlap one another.<ref>{{cite web|title=Diatoms|url=http://www.ucl.ac.uk/GeolSci/micropal/diatom.html|access-date=13 February 2016|archive-date=2 February 2016|archive-url=https://web.archive.org/web/20160202141717/http://www.ucl.ac.uk/GeolSci/micropal/diatom.html|url-status=live}}</ref> The [[biogenic silica]] composing the cell wall is [[biosynthesis|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. 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]], usually through [[meiosis]] and sexual reproduction, but exceptions exist. The auxospore expands in size to give rise to a much larger cell, which then returns to size-diminishing divisions.<ref>[https://books.google.com/books?id=xyFvEAAAQBAJ&dq=diatoms+sexual+reproduction+auxospore+frustule&pg=PA295 The Molecular Life of Diatoms]</ref>

[[File:Pennate diatom infected with two chytrid-like fungal pathogens.png|thumb|upright=1.4| [[Pennate diatom]] from an Arctic [[meltpond]], infected with two [[Chytridiomycota|chytrid-like]] [zoo-]sporangium fungal pathogens (in false-colour red). Scale bar = 10 μm.<ref>{{cite journal |doi=10.1038/s42003-020-0891-7 |title=Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean |year=2020 |last1=Kilias |first1=Estelle S. |last2=Junges |first2=Leandro |last3=Šupraha |first3=Luka |last4=Leonard |first4=Guy |last5=Metfies |first5=Katja |last6=Richards |first6=Thomas A. |journal=Communications Biology |volume=3 |issue=1 |page=183 |pmid=32317738 |pmc=7174370 |s2cid=216033140}}</ref>]]
[[File:20110123 185042 Diatom.jpg|thumb|upright=1.4| Light microscopy of a living diatom. Numbered graduations are 10 micrometres apart]]

The exact mechanism of transferring [[silica]] absorbed by the diatom to the [[cell wall]] 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]]. 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.<ref name="Thamatrakoln-2006">{{cite journal|last1=Thamatrakoln|first1=K.|title=Comparative Sequence Analysis of Diatom Silicon Transporters: Toward a Mechanistic Model of Silicon Transport|last2=Alverson|first2=A. J.|last3=Hildebrand|first3=M.|journal=Journal of Phycology|date=2006|volume=42|issue=4|pages=822–834|doi=10.1111/j.1529-8817.2006.00233.x|bibcode=2006JPcgy..42..822T |s2cid=86674657}}</ref> Silaffins, sets of polycationic [[peptides]], 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]], including a higher number of [[polyamines]] than most genomes, as well as three distinct silica transport genes.<ref>{{cite journal|last1=Kröger|first1=Nils|last2=Deutzmann|first2=Rainer|last3=Manfred|first3=Sumper|s2cid=10925689|title=Polycationic Peptides from Diatom Biosilica That Direct Silica Nanosphere Formation.|journal=Science|date=November 1999|volume=286|issue=5442|pages=1129–1132|doi=10.1126/science.286.5442.1129|pmid=10550045}}{{Dead link|date=March 2020 |bot=InternetArchiveBot |fix-attempted=yes }}</ref> In a [[phylogenetic]] study on silica transport genes from 8 diverse groups of diatoms, silica transport was found to generally group with species.<ref name="Thamatrakoln-2006" /> 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]] 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 [[Protein dimer|dimerization]].<ref name="Thamatrakoln-2006" /> 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.<ref>{{cite book|last1=Kroger|first1=Nils|title=Handbook of Biomineralization: Biological Aspects and Structure Formation|date=2007|publisher=Wiley-VCH Verlag GmbH|location=Weinheim, Germany|pages=chapter 3}}</ref> These two protein structures have been shown to create sheets of patterned silica [[in-vivo]] 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|silica-based]] [[cell wall]]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.<ref>Anonymous (1702). "Two letters from a Gentleman in the Country, relating to Mr. Leeuwenhoek's Letter in Transaction, no. 283.", ''Philos. Trans. R. Soc. Lond. B'', '''23''': 1494–1501.</ref> 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]] in a "subcolloidal" state<ref>Rogall, E. (1939). "[https://www.jstor.org/stable/23357402 Ueber den feinbau der kieselmembran der diatomeen"], ''Planta'': 279-291.</ref> 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]], [[molecular biology]], [['omics]], and [[transgenic]] 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.<ref name="Hildebrand-2018">{{cite journal | last1=Hildebrand | first1=Mark | last2=Lerch | first2=Sarah J. L. | last3=Shrestha | first3=Roshan P. | title=Understanding Diatom Cell Wall Silicification—Moving Forward | journal=Frontiers in Marine Science | publisher=Frontiers Media SA | volume=5 | date=2018-04-11 | page=125 | issn=2296-7745 | doi=10.3389/fmars.2018.00125| doi-access=free | bibcode=2018FrMaS...5..125H }} [[File:CC-BY icon.svg|50px]] Modified material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>

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]] this large structural object in a short time period, synched with [[cell cycle]] progression, necessitates substantial physical movements within the cell as well as dedication of a significant proportion of the cell's [[biosynthetic]] capacities.<ref name="Hildebrand-2018" />

The first characterisations of the biochemical processes and components involved in diatom silicification were made in the late 1990s.<ref>{{cite journal | last1=Hildebrand | first1=Mark | last2=Volcani | first2=Benjamin E. | last3=Gassmann | first3=Walter | last4=Schroeder | first4=Julian I. | title=A gene family of silicon transporters | journal=Nature | publisher=Springer Science and Business Media LLC | volume=385 | issue=6618 | year=1997 | issn=0028-0836 | doi=10.1038/385688b0 | pages=688–689| pmid=9034185 | bibcode=1997Natur.385..688H | s2cid=4266966 }}</ref><ref>{{cite journal | last1=Kröger | first1=Nils | last2=Deutzmann | first2=Rainer | last3=Sumper | first3=Manfred | title=Polycationic Peptides from Diatom Biosilica That Direct Silica Nanosphere Formation | journal=Science | publisher=American Association for the Advancement of Science (AAAS) | volume=286 | issue=5442 | date=1999-11-05 | issn=0036-8075 | doi=10.1126/science.286.5442.1129 | pages=1129–1132| pmid=10550045 }}</ref><ref>{{cite journal | last1=Kröger | first1=Nils | last2=Deutzmann | first2=Rainer | last3=Bergsdorf | first3=Christian | last4=Sumper | first4=Manfred | title=Species-specific polyamines from diatoms control silica morphology | journal=Proceedings of the National Academy of Sciences | volume=97 | issue=26 | date=2000-12-05 | issn=0027-8424 | doi=10.1073/pnas.260496497 | pages=14133–14138| pmid=11106386 | pmc=18883 | bibcode=2000PNAS...9714133K | doi-access=free }}</ref> These were followed by insights into how higher order assembly of silica structures might occur.<ref>{{cite journal | last1=Tesson | first1=Benoit | last2=Hildebrand | first2=Mark | title=Extensive and Intimate Association of the Cytoskeleton with Forming Silica in Diatoms: Control over Patterning on the Meso- and Micro-Scale | journal=PLOS ONE | publisher=Public Library of Science (PLoS) | volume=5 | issue=12 | date=2010-12-10 | issn=1932-6203 | doi=10.1371/journal.pone.0014300 | article-number=e14300| pmid=21200414 | pmc=3000822 | bibcode=2010PLoSO...514300T | doi-access=free }}</ref><ref>{{cite journal | last1=Tesson | first1=Benoit | last2=Hildebrand | first2=Mark | title=Characterization and Localization of Insoluble Organic Matrices Associated with Diatom Cell Walls: Insight into Their Roles during Cell Wall Formation | journal=PLOS ONE | publisher=Public Library of Science (PLoS) | volume=8 | issue=4 | date=2013-04-23 | issn=1932-6203 | doi=10.1371/journal.pone.0061675 | article-number=e61675| pmid=23626714 | pmc=3633991 | bibcode=2013PLoSO...861675T | doi-access=free }}</ref><ref>{{cite journal | last1=Scheffel | first1=André | last2=Poulsen | first2=Nicole | last3=Shian | first3=Samuel | last4=Kröger | first4=Nils | title=Nanopatterned protein microrings from a diatom that direct silica morphogenesis | journal=Proceedings of the National Academy of Sciences | volume=108 | issue=8 | date=2011-02-07 | issn=0027-8424 | doi=10.1073/pnas.1012842108 | pages=3175–3180| pmid=21300899 | pmc=3044418 | doi-access=free }}</ref> 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.<ref>{{cite journal | last1=Kotzsch | first1=Alexander | last2=Gröger | first2=Philip | last3=Pawolski | first3=Damian | last4=Bomans | first4=Paul H. H. | last5=Sommerdijk | first5=Nico A. J. M. | last6=Schlierf | first6=Michael | last7=Kröger | first7=Nils | title=Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization | journal=BMC Biology | publisher=Springer Science and Business Media LLC | volume=15 | issue=1 | date=2017-07-24 | page=65 | issn=1741-7007 | doi=10.1186/s12915-017-0400-8| pmid=28738898 | pmc=5525289 | doi-access=free }}</ref><ref>{{cite journal | last1=Tesson | first1=Benoit | last2=Lerch | first2=Sarah J. L. | last3=Hildebrand | first3=Mark | title=Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica | journal=Scientific Reports | publisher=Springer Science and Business Media LLC | volume=7 | issue=1 | date=2017-10-18 | page=13457 | issn=2045-2322 | doi=10.1038/s41598-017-13613-8| pmid=29044150 | pmc=5647440 | bibcode=2017NatSR...713457T }}</ref> 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.<ref name="Hildebrand-2018" />

==Behaviour==
{{Multiple image
|align=right
|image1=Den Norske Nordhavs-expedition, 1876-1878 (1880-1901) (20671468900)-47.jpg
|width1=107
|caption1=''Chaetoceros willei''<br /><small>{{smallcaps|Gran, 1897}}</small>
|image2=Den Norske Nordhavs-expedition, 1876-1878 (1880-1901) (20671468900)-48+49.jpg
|width2=200
|caption2=''Chaetoceros furcillatus'' <small>{{smallcaps|J.W.Bailey, 1856}}</small>
}}

Most centric and araphid pennate diatoms are [[Motility|nonmotile]], and their relatively dense cell walls cause them to readily sink. [[Plankton]]ic forms in open water usually rely on [[turbulence|turbulent]] 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.<ref>{{Citation|last1=Padisák|first1=Judit|date=2003|work=Aquatic Biodiversity: A Celebratory Volume in Honour of Henri J. Dumont|pages=243–257|editor-last=Martens|editor-first=Koen|series=Developments in Hydrobiology|publisher=Springer Netherlands|language=en|doi=10.1007/978-94-007-1084-9_18|isbn=978-94-007-1084-9|last2=Soróczki-Pintér|first2=Éva|last3=Rezner|first3=Zsuzsanna|title=Sinking properties of some phytoplankton shapes and the relation of form resistance to morphological diversity of plankton — an experimental study |url=http://real.mtak.hu/3305/4/1014414.pdf|access-date=4 October 2019|archive-url=https://web.archive.org/web/20180723003836/http://real.mtak.hu/3305/4/1014414.pdf|archive-date=23 July 2018}}</ref> These adaptations increase their [[Surface-area-to-volume ratio|surface area to volume ratio]] and [[Parasitic drag|drag]], allowing them to stay suspended in the water column longer. Individual cells may regulate [[buoyancy]] via an ionic pump.<ref>{{cite journal|last1=Anderson|first1=Lars W. J.|last2=Sweeney|first2=Beatrice M.|title=Diel changes in sedimentation characteristics of Ditylum brightwelli: Changes in cellular lipid and effects of respiratory inhibitors and ion-transport modifiers1|journal=Limnology and Oceanography|date=1 May 1977|volume=22|issue=3|pages=539–552|doi=10.4319/lo.1977.22.3.0539|language=en|issn=1939-5590|bibcode=1977LimOc..22..539A|doi-access=free}}</ref>

Some pennate diatoms are capable of a type of locomotion called "gliding", which allows them to move across surfaces via adhesive [[mucilage]] secreted through a seamlike structure called the raphe.<ref>{{Cite journal|last1=Poulsen|first1=Nicole C.|last2=Spector|first2=Ilan|last3=Spurck|first3=Timothy P.|last4=Schultz|first4=Thomas F.|last5=Wetherbee|first5=Richard|date=1 September 1999|title=Diatom gliding is the result of an actin-myosin motility system|journal=Cell Motility and the Cytoskeleton |language=en|volume=44|issue=1|pages=23–33|doi=10.1002/(SICI)1097-0169(199909)44:1<23::AID-CM2>3.0.CO;2-D|pmid=10470016|issn=1097-0169}}</ref><ref>{{Cite web|url=http://tolweb.org/raphid_diatoms/125307|title=raphid diatoms|last=Mann|first=David G.|date=February 2010|website=The Tree of Life Web Project|access-date=27 September 2019|archive-date=27 September 2019|archive-url=https://web.archive.org/web/20190927232025/http://tolweb.org/raphid_diatoms/125307}}</ref> 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; [[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.

[[File:Den Norske Nordhavs-expedition, 1876-1878 (1880-1901) (20671468900)-cropped.jpg|thumb|upright=1.5|left|Planktonic diatoms such as ''[[Thalassiosira]]'' sp. (56–62), ''[[Asteromphalus]]'' sp. (63), ''[[Aulacoseira]]'' sp. (64–66), and ''[[Chaetoceros]]'' (see twin image above) often grow in chains, and have features such as spines which slow sinking rates by increasing drag.]]
[[File:Diatom chain.jpg|thumb|upright=1.8| Some ''[[Thalassiosira]]'' diatoms form chain-like colonies, like these collected near the Antarctic peninsula coast by the schooner of the [[Tara expedition|''Tara'' Oceans Expedition]] for plankton research.<br />This projection of a stack of [[Confocal microscopy|confocal images]] shows the diatoms' [[cell wall]] (cyan), [[chloroplast]]s (red), [[DNA]] (blue), [[Biological membrane|membranes]] and [[organelle]]s (green).]]
{{clear}}

===Phytochromes===
Even though light is a crucial part of how diatoms create oxygen for the planet, the organism faces some difficulties when it comes to detecting its energy source. The intensity of light in water lessens as depth increases. Light penetration also greatly differs between coastal and open waters and during the changing seasons. Such factors result in a less efficient photosynthetic conversion, similar to the process of plant photosynthesis,<ref>{{Cite journal |last1=Lu |first1=Danying |last2=Liu |first2=Bin |last3=Ren |first3=Mingjie |last4=Wu |first4=Chao |last5=Ma |first5=Jingjing |last6=Shen |first6=Yamei |date=2021-10-22 |title=Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata |journal=Plants |language=en |volume=10 |issue=11 |page=2261 |doi=10.3390/plants10112261 |doi-access=free |issn=2223-7747 |pmc=8618083 |pmid=34834626|bibcode=2021Plnts..10.2261L }}</ref> as the light becomes dimmer, photsynthesis slows down. However, diatoms possess [[wiktionary:photoreceptor|photoreceptors]], which are light-activated proteins, that aid them in sensing different light wavelengths, such as red light and far-red light, for detecting light in the ocean.<ref>{{Cite journal |last1=Fortunato |first1=Antonio Emidio |last2=Jaubert |first2=Marianne |last3=Enomoto |first3=Gen |last4=Bouly |first4=Jean-Pierre |last5=Raniello |first5=Raffaella |last6=Thaler |first6=Michael |last7=Malviya |first7=Shruti |last8=Bernardes |first8=Juliana Silva |last9=Rappaport |first9=Fabrice |last10=Gentili |first10=Bernard |last11=Huysman |first11=Marie J.J. |last12=Carbone |first12=Alessandra |last13=Bowler |first13=Chris |last14=d'Alcalà |first14=Maurizio Ribera |last15=Ikeuchi |first15=Masahiko |date=2016-03-01 |title=Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean |journal=The Plant Cell |volume=28 |issue=3 |pages=616–628 |doi=10.1105/tpc.15.00928 |issn=1040-4651 |pmc=4826011 |pmid=26941092|bibcode=2016PlanC..28..616F }}</ref>

{{multiple image
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 | background color  = 
 | image1    = Phaeodactylum tricornutum.png
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 | caption1  = ''Phaeodactylum tricornutum''
 | image2    = Thalassiosira pseudonana.png
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 | caption2  = ''Thalassiosira pseudonana''
}}

It has been demonstrated that diatoms use photoreceptors called [[phytochrome]]s to determine the water's depth to respond to light signals. Phytochromes can sense red and far-red light and are widely known to be found in both plants and phytoplankton.<ref name="Duchêne-2025" /><ref>{{Cite journal |last1=Duanmu |first1=Deqiang |last2=Bachy |first2=Charles |last3=Sudek |first3=Sebastian |last4=Wong |first4=Chee-Hong |last5=Jiménez |first5=Valeria |last6=Rockwell |first6=Nathan C. |last7=Martin |first7=Shelley S. |last8=Ngan |first8=Chew Yee |last9=Reistetter |first9=Emily N. |last10=van Baren |first10=Marijke J. |last11=Price |first11=Dana C. |last12=Wei |first12=Chia-Lin |last13=Reyes-Prieto |first13=Adrian |last14=Lagarias |first14=J. Clark |last15=Worden |first15=Alexandra Z. |date=2014-11-04 |title=Marine algae and land plants share conserved phytochrome signaling systems |journal=Proceedings of the National Academy of Sciences |volume=111 |issue=44 |pages=15827–15832 |doi=10.1073/pnas.1416751111 |doi-access=free |pmc=4226090 |pmid=25267653|bibcode=2014PNAS..11115827D }}</ref> These proteins switch between two states called red-light and far red-light so that the organism can detect and respond to any changes in the perceived underwater light intensity and spectrum.<ref>{{Cite journal |last1=Cheng |first1=Mei-Chun |last2=Kathare |first2=Praveen Kumar |last3=Paik |first3=Inyup |last4=Huq |first4=Enamul |date=2021-06-17 |title=Phytochrome Signaling Networks |journal=Annual Review of Plant Biology |language=en |volume=72 |issue=  1|pages=217–244 |doi=10.1146/annurev-arplant-080620-024221 |issn=1543-5008 |pmc=10988782 |pmid=33756095|bibcode=2021AnRPB..72..217C }}</ref> Since red and far-red light is known to diminish with increasing water depth, many {{who|date=March 2025}} questioned the importance of the phytochromes' role when it comes to marine life. Analysis of  environmental DNA sequences taken from the [[Tara expedition|Tara Oceans expedition]],<ref>{{Cite journal |last1=Pesant |first1=Stéphane |last2=Not |first2=Fabrice |last3=Picheral |first3=Marc |last4=Kandels-Lewis |first4=Stefanie |last5=Le Bescot |first5=Noan |last6=Gorsky |first6=Gabriel |last7=Iudicone |first7=Daniele |last8=Karsenti |first8=Eric |last9=Speich |first9=Sabrina |last10=Troublé |first10=Romain |last11=Dimier |first11=Céline |last12=Searson |first12=Sarah |date=2015-05-26 |title=Open science resources for the discovery and analysis of Tara Oceans data |journal=Scientific Data |language=en |volume=2 |issue=1 |page=150023 |doi=10.1038/sdata.2015.23 |issn=2052-4463 |pmc=4443879 |pmid=26029378|bibcode=2015NatSD...250023. }}</ref> as well as the genome data from cultured diatoms which demonstrated that the phytochrome-encoding genes were mostly found in diatoms living in temperate and polar regions in mid-to-high latitudes<ref name="Duchêne-2025" /> but such diatom phytochrome genes were not found in diatoms living in tropical waters.

Laboratory experiments with the diatom ''[[Phaeodactylum tricornutum]]'' demonstrated how the diatom phytochromes react to light.<ref name="Duchêne-2025" /> Using a yellow fluorescent protein gene controlled by phytochromes  inserted  into the diatom enabled its activity in simulations with deep-water conditions to be tracked. This showed that diatoms had developed a reduced sensitivity to far-red light, as well as an increased sensitivity to low-intensity blue and green light, which are more present at greater depths.<ref name="Duchêne-2025">{{Cite journal |last1=Duchêne |first1=Carole |last2=Bouly |first2=Jean-Pierre |last3=Pierella Karlusich |first3=Juan José |last4=Vernay |first4=Emeline |last5=Sellés |first5=Julien |last6=Bailleul |first6=Benjamin |last7=Bowler |first7=Chris |last8=Ribera d'Alcalà |first8=Maurizio |last9=Falciatore |first9=Angela |last10=Jaubert |first10=Marianne |date=January 2025 |title=Diatom phytochromes integrate the underwater light spectrum to sense depth |url=https://www.nature.com/articles/s41586-024-08301-3 |journal=Nature |language=en |volume=637 |issue=8046 |pages=691–697 |doi=10.1038/s41586-024-08301-3 |pmid=39695224 |bibcode=2025Natur.637..691D |issn=1476-4687|url-access=subscription }}</ref>

Removal of the phytochrome gene from the diatom ''[[Thalassiosira pseudonana]]'' grown in a similar deep-water simulation demonstrated that the mutant diatom had a lower photosynthetic efficiency, as well as a reduced photoprotection, compared to the wild-type diatoms with the phytochrome gene,<ref name="Duchêne-2025" /> and that when both the mutant and wild-type diatoms were exposed to high white light, there was no difference in reactions.

With these findings, the authors found that diatom phytochromes respond more to blue and green light in low intensities, unlike the plant phytochromes that respond to red and far-red light.<ref>{{Cite journal |last1=Kreslavski |first1=Vladimir D. |last2=Los |first2=Dmitry A. |last3=Schmitt |first3=Franz-Josef |last4=Zharmukhamedov |first4=Sergey K. |last5=Kuznetsov |first5=Vladimir V. |last6=Allakhverdiev |first6=Suleyman I. |date=2018-05-01 |title=The impact of the phytochromes on photosynthetic processes |url=https://linkinghub.elsevier.com/retrieve/pii/S0005272818300367 |journal=Biochimica et Biophysica Acta (BBA) - Bioenergetics |volume=1859 |issue=5 |pages=400–408 |doi=10.1016/j.bbabio.2018.03.003 |pmid=29545089 |issn=0005-2728|url-access=subscription }}</ref> They suggest that the diatom phytochromes went through an evolutionary adaptation to acclimate to the violent waters in the open waters of the temperate and polar regions. Since the function of diatom phytochromes is to sense the water depth, it provides the diatoms information that is very advantageous in regions with differing seasons. These photoreceptors play a critical role in helping phytoplankton adjust to environments with limited light, specifically the deep-water environments.

== Life cycle ==
{{multiple image
 | align = right
 | caption_align = center
 | direction = horizontal
 | header            = Sexual reproduction
 | header_align      = center
 | header_background = 
 | width1    = 220
 | image1    = Centric diatom life-cycle.jpg
 | alt1      = 
 | caption1  = Centric diatom ([[oogamy]])
 | width2    = 207
 | image2    = Diatom pennate life cycle.jpg
 | alt2      = 
 | caption2  = Pennate diatom (morphological [[isogamy]], physiological [[anisogamy]])
}}

===Reproduction and cell size===
Reproduction among these organisms is asexual by [[binary fission]], during which the diatom divides into two parts, producing two "new" diatoms with identical genes. Each new organism receives one of the two [[frustule]]s – one larger, the other smaller – possessed by the parent, which is now called the [[Frustule#Thecae|epitheca]]; and is used to construct a second, smaller frustule, the [[Frustule#Thecae|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.<ref name="Hasle-1996" /> It has been observed, however, that certain taxa have the ability to divide without causing a reduction in cell size.<ref name="Drebes-1977">{{cite book|author=G. Drebes|editor=Dietrich Werner|title=The Biology of Diatoms|chapter-url=https://books.google.com/books?id=A4GBA7rlAroC|access-date=14 November 2013|volume=13|series=Botanical Monographs|date=1 January 1977|publisher=University of California Press|isbn=978-0-520-03400-6|pages=250–283|chapter=Chapter 9: Sexuality|archive-date=1 August 2020|archive-url=https://web.archive.org/web/20200801020328/https://books.google.com/books?id=A4GBA7rlAroC|url-status=live}}</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="Hasle-1996" />

===Cell division===
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="Rita A. Horner-2002" />

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]] restitutes cell size and prevents [[:Wiktionary:clonal|clonal]] death.<ref>Lewis, W. M., Jr. (1984). "The diatom sex clock and its evolutionary significance". ''The American Naturalist'', '''123'''(1): 73–80</ref><ref>Chepurnov VA, Mann DG, Sabbe K, Vyverman W. (2004). "Experimental studies on sexual reproduction in diatoms". In Jeon KW, ed. ''A Survey of Cell Biology''. International Review of Cytology '''237''': 91–154. London.</ref><ref>Drebes (1977) "Sexuality". In: Werner D, ed. ''The Biology of Diatoms'', Botanical Monographs '''13''' 250–283. Oxford: Blackwell Scientific Publications.</ref><ref>{{cite journal | title=Size reduction, reproductive strategy and the life cycle of a centric diatom | journal=Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences | publisher=The Royal Society | volume=336 | issue=1277 | date=1992-05-29 | issn=0962-8436 | doi=10.1098/rstb.1992.0056 | pages=191–213 | s2cid=86332060 | ref={{sfnref | The Royal Society}}}}</ref><ref>{{cite journal | last1=Koester | first1=Julie A. | last2=Brawley | first2=Susan H. | last3=Karp-Boss | first3=Lee | last4=Mann | first4=David G. | title=Sexual reproduction in the marine centric diatom Ditylum brightwellii (Bacillariophyta) | journal=European Journal of Phycology | publisher=Informa UK Limited | volume=42 | issue=4 | year=2007 | issn=0967-0262 | doi=10.1080/09670260701562100 | pages=351–366| s2cid=80737380 | doi-access=free | bibcode=2007EJPhy..42..351K }}</ref> The entire lifecycles of only a few diatoms have been described and rarely have sexual events been captured in the environment.<ref name="Moore-2017" />

===Sexual reproduction===

Most [[eukaryote]]s are capable of [[sexual reproduction]] involving [[meiosis]].  Sexual reproduction appears to be an obligatory phase in the life cycle of diatoms, particularly as cell size decreases with successive vegetative divisions.<ref name="Mouget-2009">{{cite journal |vauthors=Mouget JL, Gastineau R, Davidovich O, Gaudin P, Davidovich NA |title=Light is a key factor in triggering sexual reproduction in the pennate diatom ''Haslea ostrearia'' |journal=FEMS Microbiol Ecol |volume=69 |issue=2 |pages=194–201 |date=August 2009 |pmid=19486155 |doi=10.1111/j.1574-6941.2009.00700.x |bibcode=2009FEMME..69..194M }}</ref>  Sexual reproduction involves production of [[gamete]]s and the fusion of gametes to form a [[zygote]] in which maximal cell size is restored.<ref name="Mouget-2009"/>  The signaling that triggers the sexual phase is favored when cells accumulate together, so that the distance between them is reduced and the contacts and/or the perception of chemical cues is facilitated.<ref>{{cite journal |vauthors=Scalco E, Stec K, Iudicone D, Ferrante MI, Montresor M |title=The dynamics of sexual phase in the marine diatom ''Pseudo-nitzschia multistriata'' (Bacillariophyceae) |journal=J Phycol |volume=50 |issue=5 |pages=817–28 |date=October 2014 |pmid=26988637 |doi=10.1111/jpy.12225 |bibcode=2014JPcgy..50..817S }}</ref>

An exploration of the [[genome]]s of five diatoms and one diatom [[transcriptome]] led to the identification of 42 [[gene]]s potentially involved in meiosis.<ref name="Patil-2015">{{cite journal |vauthors=Patil S, Moeys S, von Dassow P, Huysman MJ, Mapleson D, De Veylder L, Sanges R, Vyverman W, Montresor M, Ferrante MI |title=Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species ''Pseudo-nitzschia multistriata'' and ''Seminavis robusta'' |journal=BMC Genomics |volume=16 |issue= |article-number=930 |date=November 2015 |pmid=26572248 |pmc=4647503 |doi=10.1186/s12864-015-1983-5 |doi-access=free}}<br/>{{cite journal |vauthors=Patil S, Moeys S, von Dassow P, Huysman MJ, Mapleson D, De Veylder L, Sanges R, Vyverman W, Montresor M, Ferrante MI |title=Correction to: Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species ''Pseudo-nitzschia multistriata'' and ''Seminavis robusta'' |journal=BMC Genomics |volume=20 |issue=1 |article-number=544 |date=July 2019 |pmid=31277569 |pmc=6610888 |doi=10.1186/s12864-019-5942-4 |doi-access=free}}</ref>  Thus a meiotic toolkit appears to be conserved in these six diatom species,<ref name="Patil-2015"/> indicating a central role of meiosis in diatoms as in other eukaryotes.

===Sperm motility===
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="Rita A. Horner-2002" /> 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|isogamous]]).<ref name="Hasle-1996" /> Certain araphid species, that is pennate diatoms without a [[raphe]] (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.<ref name="Drebes-1977" />

=== 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]] enzymes to break down the organic algal material.<ref>{{cite journal |doi=10.1038/17351 |id={{INIST|1755031}} |year=1999 |last1=Azam |first1=Farooq |title=Accelerated dissolution of diatom silica by marine bacterial assemblages |journal=Nature |volume=397 |issue=6719 |pages=508–12 |last2=Bidle |first2=Kay D. |bibcode=1999Natur.397..508B |s2cid=4397909 }}</ref><ref>{{cite journal |doi=10.1371/journal.pone.0059977 |pmid=23560063 |pmc=3613400 |title=The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal |journal=PLOS ONE |volume=8 |issue=4 |article-number=e59977 |year=2013 |last1=Zakharova |first1=Yulia R. |last2=Galachyants |first2=Yuri P. |last3=Kurilkina |first3=Maria I. |last4=Likhoshvay |first4=Alexander V. |last5=Petrova |first5=Darya P. |last6=Shishlyannikov |first6=Sergey M. |last7=Ravin |first7=Nikolai V. |last8=Mardanov |first8=Andrey V. |last9=Beletsky |first9=Alexey V. |last10=Likhoshway |first10=Yelena V. |bibcode=2013PLoSO...859977Z |doi-access=free }}</ref>

== Ecology ==
{{plankton sidebar|taxonomy}}
[[File:Diatoms+Abundance.png|thumb|upright=1.7|right| {{center|Regions of high abundance of diatoms in the ocean}}]]
[[File:Diatoms Egge and Aksnes 1992 plot.png|thumb|upright=1.7|right| {{center|Diatom dominance (as a percentage of total cell
counts)<br />versus silicate concentration <ref name="Egge-1992">{{cite journal |last1=Egge |first1=J. K. |last2=Aksnes |first2=D. L. |year=1992 |title=Silicate as regulating nutrient in phytoplankton competition |journal=Mar. Ecol. Prog. Ser. |volume=83 |pages=281–289 |doi=10.3354/meps083281 |bibcode=1992MEPS...83..281E |doi-access=free}}</ref>}}]]

===Distribution===

Diatoms are a widespread group and can be found in the [[ocean]]s, in [[fresh water]], in [[soil]]s, and on damp surfaces. They are one of the dominant components of [[phytoplankton]] in nutrient-rich coastal waters and during oceanic spring blooms, since they can divide more rapidly than other groups of phytoplankton.<ref name="Furnas-1990" /> 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 a 2003 study found that they contribute an estimated 45% of the total oceanic [[primary production]] of organic material.<ref name="Yool-2003">{{cite journal |doi=10.1029/2002GB002018 |title=Role of diatoms in regulating the ocean's silicon cycle |journal=Global Biogeochemical Cycles |volume=17 |issue=4 |year=2003 |last1=Yool |first1=Andrew |last2=Tyrrell |first2=Toby |pages=n/a |bibcode=2003GBioC..17.1103Y |citeseerx=10.1.1.394.3912 |s2cid=16849373 }}</ref> However, a more recent 2016 study estimates that the number is closer to 20%.<ref>{{Cite journal |last1=Malviya |first1=Shruti |last2=Scalco |first2=Eleonora |last3=Audic |first3=Stéphane |last4=Vincent |first4=Flora |last5=Veluchamy |first5=Alaguraj |last6=Poulain |first6=Julie |last7=Wincker |first7=Patrick |last8=Iudicone |first8=Daniele |last9=de Vargas |first9=Colomban |last10=Bittner |first10=Lucie |last11=Zingone |first11=Adriana |last12=Bowler |first12=Chris |date=2016-02-29 |title=Insights into global diatom distribution and diversity in the world's ocean |journal=Proceedings of the National Academy of Sciences |volume=113 |issue=11 |pages=E1516–E1525 |doi=10.1073/pnas.1509523113 |doi-access=free |pmid=26929361 |issn=0027-8424|pmc=4801293 |bibcode=2016PNAS..113E1516M }}</ref> Spatial distribution of marine phytoplankton species is restricted both horizontally and vertically.<ref>{{cite journal |doi=10.2307/2406711 |pmid=28563010 |jstor=2406711 |title=Plankton Evolution |journal=Evolution |volume=24 |issue=1 |pages=1–22 |year=1970 |last1=Lipps |first1=Jere H. }}</ref><ref name="Rita A. Horner-2002">{{cite book|author=Rita A. Horner|title=A taxonomic guide to some common marine phytoplankton|url=https://books.google.com/books?id=JU8VAQAAIAAJ|access-date=13 November 2013|year=2002|publisher=Biopress|isbn=978-0-948737-65-7|pages=25–30|archive-date=1 August 2020|archive-url=https://web.archive.org/web/20200801020312/https://books.google.com/books?id=JU8VAQAAIAAJ|url-status=live}}</ref>

===Growth===
[[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 (as at the [[Spring (season)|spring]]), their competitive edge and rapid growth rate<ref name="Furnas-1990">{{cite journal |doi=10.1093/plankt/12.6.1117 |id={{INIST|5474600}} |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=1117–51 |year=1990 |last1=Furnas |first1=Miles J. }}</ref> enables them to 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'').

===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]] 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"]. {{webarchive|url=https://web.archive.org/web/20151007110108/http://alienspecies.royalbcmuseum.bc.ca/eng/species/didymo-rock-snot |date=7 October 2015 }} Virtual Exhibit of the [[Virtual Museum of Canada]]</ref><ref>{{Cite web |url=http://www.ct.gov/deep/cwp/view.asp?A=4013&Q=476204 |title=DEP Reports Didymo Discovered in the West Branch Farmington River |access-date=27 April 2015 |archive-url=https://web.archive.org/web/20150216015753/http://www.ct.gov/deep/cwp/view.asp?A=4013&Q=476204 |archive-date=16 February 2015 }}</ref> The problem is most frequently recorded from [[Australia]] and [[Didymo in New Zealand|New Zealand]].<ref>{{cite web |title=Didymo Stakeholder Update – 31 October 2008 |url=http://www.biosecurity.govt.nz/pests/didymo/update-31-10-08 |archive-url=https://web.archive.org/web/20130212200059/http://www.biosecurity.govt.nz/pests/didymo/update-31-10-08 |archive-date=12 February 2013 |access-date=1 December 2013 |publisher=MAF Biosecurity New Zealand}}</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="Dugdale-1998">{{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 | journal=Nature | volume=391 | issue=6664| pages=270–273 | doi=10.1038/34630|bibcode=1998Natur.391..270D | s2cid=4394149 }}</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 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]] 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="Dugdale-1998" /><ref name="Smetacek-1985">{{cite journal | last1=Smetacek | first1=V. S. | year=1985 | title=Role of sinking in diatom life-history cycles: Ecological, evolutionary and geological significance | journal=Mar. Biol. | volume=84 | issue=3| pages=239–251 | doi=10.1007/BF00392493 | bibcode=1985MarBi..84..239S | s2cid=85054779 }}</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="Yool-2003" /><ref name="Treguer-1995" />

===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.{{Citation needed|date=February 2016}} The use of silicon by diatoms is believed by many researchers to be the key to this ecological success. Raven (1983)<ref name="Raven-1983">{{cite journal | last1=Raven | first1=J. A. | year=1983 | title=The transport and function of silicon in plants | journal=Biol. Rev. | volume=58 | issue=2| pages=179–207 | doi=10.1111/j.1469-185X.1983.tb00385.x| s2cid=86067386 }}</ref> noted that, relative to organic [[cell wall]]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)<ref name="Egge-1992" /> found that diatom [[ecological dominance|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. Other researchers<ref name="Milligan-2002">{{cite journal | last1=Milligan | first1=A. J. | last2=Morel | first2=F. M. M. | year=2002 | title=A proton buffering role for silica in diatoms | journal=Science | volume=297 | issue=5588| pages=1848–1850 | doi=10.1126/science.1074958 | pmid=12228711|bibcode=2002Sci...297.1848M | s2cid=206507070 }}</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). 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.<ref name="Furnas-1990" />

===Sources for collection===
{{Further|topic=the genus of filamentous diatoms|Oscillaria}}
Diatoms can be obtained from multiple sources.<ref name="Chamberlain">Chamberlain, C. J. (1901) ''Methods in Plant Histology'', University of Chicago Press.</ref> Marine diatoms can be collected by direct water sampling, and benthic forms can be secured by scraping [[barnacle]]s, [[oyster]] 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]]'' is frequently covered with ''[[Cocconeis]]'', an elliptically shaped diatom; ''[[Vaucheria]]'' is often covered with small forms. 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. 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.<ref name="Chamberlain" />

==Biogeochemistry==
<gallery mode="packed" style="float:right" heights="400px">
File:Oceanic Silicon Cycle Budget.svg|'''The modern oceanic silicon cycle'''<br /><small>{{space|9}}Fluxes are in [[Tera-|T]][[Mole (unit)|mol]] Si y<sup>−1</sup> (1 Tmol = 28 million [[tonne|metric tons]] of silicon)</small>
</gallery>

===Silica cycle===
{{Further|Silica cycle}}

The diagram shows the major [[flux]]es of [[silicon]] in the current ocean. Most [[biogenic silica]] in the ocean ([[silica]] produced by [[biomineralisation|biological activity]]) comes from diatoms. Diatoms extract dissolved [[silicic acid]] from surface waters as they grow, and return it to the [[water column]] when they die. Inputs of silicon arrive from above via [[aeolian dust]], from the coasts via rivers, and from below via [[seafloor sediment]] recycling, weathering, and [[hydrothermal vent|hydrothermal activity]].<ref name="Treguer-1995">{{cite journal |doi=10.1126/science.268.5209.375 |pmid=17746543 |title=The Silica Balance in the World Ocean: A Reestimate |journal=Science |volume=268 |issue=5209 |pages=375–9 |year=1995 |last1=Treguer |first1=P. |last2=Nelson |first2=D. M. |last3=Van Bennekom |first3=A. J. |last4=Demaster |first4=D. J. |last5=Leynaert |first5=A. |last6=Queguiner |first6=B. |bibcode=1995Sci...268..375T |s2cid=5672525 }}</ref>

Although diatoms may have existed since the [[Triassic]], the timing of their ascendancy and "take-over" of the silicon cycle occurred more recently. 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="Penelope J. Boston-1993">{{cite book |author1=R. Siever |author2=Stephen Henry Schneider |author3=Penelope J. Boston |title=Scientists on Gaia |chapter-url=https://books.google.com/books?id=h83nGwAACAAJ |access-date=14 November 2013 |date=January 1993 |publisher=[[MIT Press]] |isbn=978-0-262-69160-4 |pages=[https://archive.org/details/scientistsongaia0000unse/page/287 287–295] |chapter=Silica in the oceans: biological-geological interplay |url-access=registration |url=https://archive.org/details/scientistsongaia0000unse/page/287}}</ref><ref>{{cite journal |doi=10.1086/320794 |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=509–22 |year=2001 |last1=Kidder |first1=David L. |last2=Erwin |first2=Douglas H. |bibcode=2001JG....109..509K |s2cid=128401816 }}</ref><ref name="Grenne-2003">{{cite journal |doi=10.1130/0091-7613(2003)031<0319:PAMSRS>2.0.CO;2 |id={{INIST|14692468}} |year=2003 |volume=31 |issue=4 |pages=319–22 |title=Paleozoic and Mesozoic silica-rich seawater: Evidence from hematitic chert (jasper) deposits |journal=Geology |last1=Grenne |first1=Tor |last2=Slack |first2=John F. |bibcode=2003Geo....31..319G }}</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 |doi=10.1016/S0012-8252(00)00024-6 |title=Radiolarian palaeoecology and radiolarites: Is the present the key to the past? |journal=Earth-Science Reviews |volume=52 |issue=1 |pages=83–120 |year=2000 |last1=Racki |first1=G |last2=Cordey |first2=Fabrice |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" remains 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="Maldonado-1999">{{cite journal |doi=10.1038/44560 |id={{INIST|1990263}} |year=1999 |last1=Maldonado |first1=Manuel |title=Decline in Mesozoic reef-building sponges explained by silicon limitation |journal=Nature |volume=401 |issue=6755 |pages=785–8 |last2=Carmona |first2=M. Carmen |last3=Uriz |first3=María J. |last4=Cruzado |first4=Antonio |bibcode=1999Natur.401..785M |s2cid=205034177 }}</ref> 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]] (66 Ma to present).<ref>{{cite journal |doi=10.1130/0091-7613(1975)3<175:SDACRE>2.0.CO;2 |year=1975 |volume=3 |issue=4 |pages=175–177 |title=Silica, diatoms, and Cenozoic radiolarian evolution |journal=Geology |last1=Harper |first1=Howard E. |last2=Knoll |first2=Andrew H. |bibcode=1975Geo.....3..175H }}</ref>
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<gallery mode="packed" style="float:right" heights="400px">
File:Ocean carbon cycle and diatom carbon dioxide concentration mechanisms 2.jpg|alt=Ocean carbon cycle and diatom carbon dioxide concentration mechanisms|Ocean carbon cycle and diatom carbon dioxide concentration mechanisms{{hsp}}<ref name="Pierella Karlusich-2021">{{cite journal | last1=Pierella Karlusich | first1=Juan José | last2=Bowler | first2=Chris | last3=Biswas | first3=Haimanti | title=Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans | journal=Frontiers in Plant Science | publisher=Frontiers Media SA | volume=12 | date=2021-04-30 | article-number=657821 | issn=1664-462X | doi=10.3389/fpls.2021.657821| pmid=33995455 | pmc=8119650 | doi-access=free }} [[File:CC-BY icon.svg|50px]] Modified material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>
</gallery>

===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 CO<sub>2</sub> emission to the atmosphere (mainly generated by fossil fuel burning and deforestation) is nearly 11 [[gigatonne]] 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]] ({{chem|H|C|O|3|-}}) and [[carbonate]] ions ({{chem|CO|3|2-}}) constitute nearly 90 and <10% of [[dissolved inorganic carbon]] (DIC) respectively, while dissolved CO<sub>2</sub> (CO<sub>2</sub> aqueous) contributes <1%. Despite this low level of CO<sub>2</sub> in the ocean and its slow [[diffusion rate]] in water, diatoms fix 10–20 GtC annually via photosynthesis thanks to their [[carbon dioxide concentrating mechanism]]s, allowing them to sustain [[marine food chain]]s. In addition, 0.1–1% of this organic material produced in the [[euphotic zone|euphotic layer]] sinks down as particles, thus transferring the surface carbon toward the deep ocean and [[Carbon sequestration|sequestering atmospheric CO<sub>2</sub>]] for thousands of years or longer. The remaining [[organic matter]] is [[Remineralisation|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 CO<sub>2</sub> to be removed from the [[carbon cycle]] for very long period.<ref name="Friedlingstein-2020">{{cite journal | last1=Friedlingstein | first1=Pierre | last2=O'Sullivan | first2=Michael | last3=Jones | first3=Matthew W. | last4=Andrew | first4=Robbie M. | last5=Hauck | first5=Judith | last6=Olsen | first6=Are | last7=Peters | first7=Glen P. | last8=Peters | first8=Wouter | last9=Pongratz | first9=Julia | last10=Sitch | first10=Stephen | last11=Le Quéré | first11=Corinne | last12=Canadell | first12=Josep G. | last13=Ciais | first13=Philippe | last14=Jackson | first14=Robert B. | last15=Alin | first15=Simone | last16=Aragão | first16=Luiz E. O. C. | last17=Arneth | first17=Almut | last18=Arora | first18=Vivek | last19=Bates | first19=Nicholas R. | last20=Becker | first20=Meike | last21=Benoit-Cattin | first21=Alice | last22=Bittig | first22=Henry C. | last23=Bopp | first23=Laurent | last24=Bultan | first24=Selma | last25=Chandra | first25=Naveen | last26=Chevallier | first26=Frédéric | last27=Chini | first27=Louise P. | last28=Evans | first28=Wiley | last29=Florentie | first29=Liesbeth | last30=Forster | first30=Piers M. | last31=Gasser | first31=Thomas | last32=Gehlen | first32=Marion | last33=Gilfillan | first33=Dennis | last34=Gkritzalis | first34=Thanos | last35=Gregor | first35=Luke | last36=Gruber | first36=Nicolas | last37=Harris | first37=Ian | last38=Hartung | first38=Kerstin | last39=Haverd | first39=Vanessa | last40=Houghton | first40=Richard A. | last41=Ilyina | first41=Tatiana | last42=Jain | first42=Atul K. | last43=Joetzjer | first43=Emilie | last44=Kadono | first44=Koji | last45=Kato | first45=Etsushi | last46=Kitidis | first46=Vassilis | last47=Korsbakken | first47=Jan Ivar | last48=Landschützer | first48=Peter | last49=Lefèvre | first49=Nathalie | last50=Lenton | first50=Andrew | last51=Lienert | first51=Sebastian | last52=Liu | first52=Zhu | last53=Lombardozzi | first53=Danica | last54=Marland | first54=Gregg | last55=Metzl | first55=Nicolas | last56=Munro | first56=David R. | last57=Nabel | first57=Julia E. M. S. | last58=Nakaoka | first58=Shin-Ichiro | last59=Niwa | first59=Yosuke | last60=O'Brien | first60=Kevin | last61=Ono | first61=Tsuneo | last62=Palmer | first62=Paul I. | last63=Pierrot | first63=Denis | last64=Poulter | first64=Benjamin | last65=Resplandy | first65=Laure | last66=Robertson | first66=Eddy | last67=Rödenbeck | first67=Christian | last68=Schwinger | first68=Jörg | last69=Séférian | first69=Roland | last70=Skjelvan | first70=Ingunn | last71=Smith | first71=Adam J. P. | last72=Sutton | first72=Adrienne J. | last73=Tanhua | first73=Toste | last74=Tans | first74=Pieter P. | last75=Tian | first75=Hanqin | last76=Tilbrook | first76=Bronte | last77=van der Werf | first77=Guido | last78=Vuichard | first78=Nicolas | last79=Walker | first79=Anthony P. | last80=Wanninkhof | first80=Rik | last81=Watson | first81=Andrew J. | last82=Willis | first82=David | last83=Wiltshire | first83=Andrew J. | last84=Yuan | first84=Wenping | last85=Yue | first85=Xu | last86=Zaehle | first86=Sönke | title=Global Carbon Budget 2020 | journal=Earth System Science Data | publisher=Copernicus GmbH | volume=12 | issue=4 | date=2020-12-11 | issn=1866-3516 | doi=10.5194/essd-12-3269-2020 | pages=3269–3340| bibcode=2020ESSD...12.3269F | display-authors=4| doi-access=free | hdl=10871/126892 | hdl-access=free }}</ref><ref name="Pierella Karlusich-2021" />

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<gallery mode="packed" style="float:right" heights="300px">
File:Urea cycle in a diatom.jpg|alt=Mitochondrial urea cycle in a generic diatom cell and the potential fates of urea cycle intermediates| Mitochondrial urea cycle in a generic diatom cell and the potential fates of urea cycle intermediates{{hsp}}<ref name="Glibert-2015">{{cite journal | last1=Glibert | first1=Patricia M. | last2=Wilkerson | first2=Frances P. | last3=Dugdale | first3=Richard C. | last4=Raven | first4=John A. | last5=Dupont | first5=Christopher L. | last6=Leavitt | first6=Peter R. | last7=Parker | first7=Alexander E. | last8=Burkholder | first8=JoAnn M. | last9=Kana | first9=Todd M. | display-authors = 6 | title=Pluses and minuses of ammonium and nitrate uptake and assimilation by phytoplankton and implications for productivity and community composition, with emphasis on nitrogen-enriched conditions | journal=Limnology and Oceanography | publisher=Wiley | volume=61 | issue=1 | date=2015-10-11 | issn=0024-3590 | doi=10.1002/lno.10203 | pages=165–197| s2cid=16561857 }} [[File:CC-BY icon.svg|50px]] Modified material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>
</gallery>

===Urea cycle===
A feature of diatoms is the [[urea cycle]], 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.<ref>{{cite journal |doi=10.1038/nature10074 |pmid=21562560 |title=Evolution and metabolic significance of the urea cycle in photosynthetic diatoms |journal=Nature |volume=473 |issue=7346 |pages=203–7 |year=2011 |last1=Allen |first1=Andrew E. |last2=Dupont |first2=Christopher L. |last3=Oborník |first3=Miroslav |last4=Horák |first4=Aleš |last5=Nunes-Nesi |first5=Adriano |last6=McCrow |first6=John P. |last7=Zheng |first7=Hong |last8=Johnson |first8=Daniel A. |last9=Hu |first9=Hanhua |last10=Fernie |first10=Alisdair R. |last11=Bowler |first11=Chris | display-authors = 6 | bibcode=2011Natur.473..203A |s2cid=4350884 |url=http://www.locus.ufv.br/handle/123456789/22722 |access-date=20 May 2021 |archive-date=19 February 2022 |archive-url=https://web.archive.org/web/20220219150348/https://www.locus.ufv.br/handle/123456789/22722 |url-status=live}}
*{{cite press release |date=12 May 2011 |title=Animal-like urea cycle in ocean's tiny diatoms enables marine phytoplankton to use carbon and nitrogen from their environment |website=ScienceDaily |url=https://www.sciencedaily.com/releases/2011/05/110511133553.htm}}</ref>

While often overlooked in photosynthetic organisms, the [[mitochondria]] also play critical roles in energy balance. Two nitrogen-related pathways are relevant and they may also change under [[ammonium]] ({{chem|NH|4|+}}) nutrition compared with [[nitrate]] ({{chem|NO|3|−}}) nutrition. First, in diatoms, and likely some other algae, there is a urea cycle.<ref name="Armbrust-2004b">{{cite journal | last1=Armbrust | first1=E. Virginia | last2=Berges | first2=John A. | last3=Bowler | first3=Chris | last4=Green | first4=Beverley R. | last5=Martinez | first5=Diego | last6=Putnam | first6=Nicholas H. | last7=Zhou | first7=Shiguo | last8=Allen | first8=Andrew E. | last9=Apt | first9=Kirk E. | last10=Bechner | first10=Michael | last11=Brzezinski | first11=Mark A. | last12=Chaal | first12=Balbir K. | last13=Chiovitti | first13=Anthony | last14=Davis | first14=Aubrey K. | last15=Demarest | first15=Mark S. | last16=Detter | first16=J. Chris | last17=Glavina | first17=Tijana | last18=Goodstein | first18=David | last19=Hadi | first19=Masood Z. | last20=Hellsten | first20=Uffe | last21=Hildebrand | first21=Mark | last22=Jenkins | first22=Bethany D. | last23=Jurka | first23=Jerzy | last24=Kapitonov | first24=Vladimir V. | last25=Kröger | first25=Nils | last26=Lau | first26=Winnie W. Y. | last27=Lane | first27=Todd W. | last28=Larimer | first28=Frank W. | last29=Lippmeier | first29=J. Casey | last30=Lucas | first30=Susan | last31=Medina | first31=Mónica | last32=Montsant | first32=Anton | last33=Obornik | first33=Miroslav | last34=Parker | first34=Micaela Schnitzler | last35=Palenik | first35=Brian | last36=Pazour | first36=Gregory J. | last37=Richardson | first37=Paul M. | last38=Rynearson | first38=Tatiana A. | last39=Saito | first39=Mak A. | last40=Schwartz | first40=David C. | last41=Thamatrakoln | first41=Kimberlee | last42=Valentin | first42=Klaus | last43=Vardi | first43=Assaf | last44=Wilkerson | first44=Frances P. | last45=Rokhsar | first45=Daniel S. | display-authors = 6 | title=The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism | journal=Science | publisher=American Association for the Advancement of Science (AAAS) | volume=306 | issue=5693 | year=2004 | issn=0036-8075 | doi=10.1126/science.1101156 | pages=79–86| pmid=15459382 | bibcode=2004Sci...306...79A | s2cid=8593895 | url=https://digital.library.unt.edu/ark:/67531/metadc783254/ | url-access=subscription }}</ref><ref name="Allen-2011">{{cite journal | last1=Allen | first1=Andrew E. | last2=Dupont | first2=Christopher L. | last3=Oborník | first3=Miroslav | last4=Horák | first4=Aleš | last5=Nunes-Nesi | first5=Adriano | last6=McCrow | first6=John P. | last7=Zheng | first7=Hong | last8=Johnson | first8=Daniel A. | last9=Hu | first9=Hanhua | last10=Fernie | first10=Alisdair R. | last11=Bowler | first11=Chris | display-authors=6 | title=Evolution and metabolic significance of the urea cycle in photosynthetic diatoms | journal=Nature | publisher=Springer Science and Business Media LLC | volume=473 | issue=7346 | year=2011 | issn=0028-0836 | doi=10.1038/nature10074 | pages=203–207 | pmid=21562560 | bibcode=2011Natur.473..203A | s2cid=4350884 | url=http://repositorio.uptc.edu.co/handle/001/3087 | archive-date=17 October 2022 | access-date=25 November 2022 | archive-url=https://web.archive.org/web/20221017100343/https://repositorio.uptc.edu.co/handle/001/3087 }}</ref><ref>{{cite journal | last1=Weyman | first1=Philip D. | last2=Beeri | first2=Karen | last3=Lefebvre | first3=Stephane C. | last4=Rivera | first4=Josefa | last5=McCarthy | first5=James K. | last6=Heuberger | first6=Adam L. | last7=Peers | first7=Graham | last8=Allen | first8=Andrew E. | last9=Dupont | first9=Christopher L. | display-authors = 6 | title=Inactivation of P haeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis | journal=Plant Biotechnology Journal | publisher=Wiley | volume=13 | issue=4 | date=2014-10-10 | issn=1467-7644 | doi=10.1111/pbi.12254 | pages=460–470| pmid=25302562 | doi-access=free }}</ref> The long-known function of the urea cycle in animals is to excrete excess nitrogen produced by [[Amino acid#Catabolism|amino acid Catabolism]]; like [[photorespiration]], 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]], and potentially the [[plastid]]{{hsp}}<ref>{{cite journal | last1=Bender | first1=Sara J. | last2=Parker | first2=Micaela S. | last3=Armbrust | first3=E. Virginia | title=Coupled Effects of Light and Nitrogen Source on the Urea Cycle and Nitrogen Metabolism over a Diel Cycle in the Marine Diatom Thalassiosira pseudonana | journal=Protist | publisher=Elsevier BV | volume=163 | issue=2 | year=2012 | issn=1434-4610 | doi=10.1016/j.protis.2011.07.008 | pages=232–251| pmid=21873112 }}</ref> and may help to regulate ammonium metabolism.<ref name="Armbrust-2004b" /><ref name="Allen-2011" /> Because of this cycle, marine diatoms, in contrast to [[chlorophyte]]s, also have acquired a mitochondrial [[urea transporter]] and, in fact, based on [[bioinformatics]], a complete mitochondrial [[Glutamate synthase|GS-GOGAT]] cycle has been hypothesised.<ref name="Allen-2011" /><ref name="Glibert-2015" />
{{clear}}

===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.<ref>{{Cite journal|last1=Armstrong|first1=E|last2=Rogerson|first2=A|last3=Leftley|first3=Jw|date=2000|title=Utilisation of seaweed carbon by three surface-associated heterotrophic protists, Stereomyxa ramosa, Nitzschia alba and Labyrinthula sp.|journal=Aquatic Microbial Ecology|language=en|volume=21|pages=49–57|doi=10.3354/ame021049|issn=0948-3055|doi-access=free}}</ref><ref>{{Cite journal|last1=Lewin|first1=Joyce|last2=Lewin|first2=R. A.|date=1967|title=Culture and Nutrition of Some Apochlorotic Diatoms of the Genus Nitzschia|journal=Microbiology|volume=46|issue=3|pages=361–367|doi=10.1099/00221287-46-3-361|issn=1350-0872|doi-access=free}}</ref>

Photosynthetic diatoms that find themselves in an environment absent of oxygen and/or sunlight can switch to anaerobic respiration known as [[Dissimilatory nitrate reduction to ammonium|nitrate respiration]] (DNRA), and stay dormant for up till months and decades.<ref>{{cite journal | pmid=21402908 | year=2011 | last1=Kamp | first1=A. | last2=De Beer | first2=D. | last3=Nitsch | first3=J. L. | last4=Lavik | first4=G. | last5=Stief | first5=P. | title=Diatoms respire nitrate to survive dark and anoxic conditions | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=108 | issue=14 | pages=5649–5654 | doi=10.1073/pnas.1015744108 | pmc=3078364 | bibcode=2011PNAS..108.5649K | doi-access=free }}</ref><ref>{{Cite journal |title=Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat |year=2021 |doi=10.1111/1462-2920.15345 |last1=Merz |first1=Elisa |last2=Dick |first2=Gregory J. |last3=Beer |first3=Dirk |last4=Grim |first4=Sharon |last5=Hübener |first5=Thomas |last6=Littmann |first6=Sten |last7=Olsen |first7=Kirk |last8=Stuart |first8=Dack |last9=Lavik |first9=Gaute |last10=Marchant |first10=Hannah K. |last11=Klatt |first11=Judith M. | display-authors = 6 | journal=Environmental Microbiology |volume=23 |issue=3 |pages=1422–1435 |pmid=33264477 |s2cid=227259897 |doi-access=free |bibcode=2021EnvMi..23.1422M |hdl=2027.42/167035 |hdl-access=free }}</ref>

Major [[pigment]]s of diatoms are [[chlorophylls]] a and c, [[beta-carotene]], [[fucoxanthin]], diatoxanthin and diadinoxanthin.<ref name="Hasle-1996" />

==Taxonomy==
[[File:Diatomeas w.jpg|thumb|right|{{center|Light microscopy of several species of living freshwater diatoms}}]]
[[File:Detail, CSIRO ScienceImage 7632 SEM diatom (cropped).jpg|thumb|{{center|Centric diatom}}]]
[[File:CSIRO ScienceImage 7233 diatom.jpg|thumb|{{center|Linked diatoms}}]]
[[File:"Diatoms cake". Typical diatom species - Stephanodiscus hantzschii Grunow in Cleve & Grunow.JPG|thumb| {{center|[[Thalassiosirales]]<br />''Stephanodiscus hantzschii''}}]]
[[File:Diatom - Isthmia nervosa - 400x (16237138292).jpg|thumb| {{center|[[Coscinodiscophyceae]]<br />''Isthmia nervosaIsthmia nervosa''}}]]
[[File:Odontella aurita cells.jpg|thumb| {{center|[[Coscinodiscophyceae]]<br />''Odontella aurita''}}]]
{{main|Taxonomy of diatoms}}

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]]s, [[chrysophyte]]s, [[chromist]]s or [[stramenopile]]s. Many are [[autotroph]]s such as [[golden alga]]e and [[kelp]]; and [[heterotroph]]s such as [[water mould]]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 (botany)|division]], [[phylum]], [[Kingdom (taxonomy)|kingdom]], or something intermediate to those. Consequently, diatoms are ranked anywhere from a [[Class (biology)|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 taxon|extant]] diatom [[species]] are believed to exist, of which around 12,000 have been named to date according to Guiry, 2012<ref>{{cite journal |doi=10.1111/j.1529-8817.2012.01222.x|title=How many species of algae are there? |journal=Journal of Phycology |volume=48 |issue=5 |pages=1057–1063 |year=2012 |last1=Guiry |first1=M. D. |pmid=27011267|bibcode=2012JPcgy..48.1057G |s2cid= 30911529}}</ref> (other sources give a wider range of estimates<ref name="Hasle-1996">{{cite book|first1=Grethe R. |last1=Hasle|first2=Erik E. |last2=Syvertsen|first3=Karen A. |last3=Steidinger|first4=Karl |last4=Tangen|editor-first=Carmelo R. |editor-last=Tomas|title=Identifying Marine Diatoms and Dinoflagellates|chapter-url=https://books.google.com/books?id=KQxPtwonlqoC|access-date=13 November 2013|date=25 January 1996|publisher=Academic Press|isbn=978-0-08-053441-1|pages=5–385|chapter=Marine Diatoms|archive-date=3 January 2014|archive-url=https://web.archive.org/web/20140103085057/http://books.google.com/books?id=KQxPtwonlqoC|url-status=live}}</ref><ref name="Round-1990">{{cite book|first1=Frank Eric |last1=Round|first2=R. M. |last2=Crawford|first3=D. G. |last3=Mann|title=The Diatoms: Biology & Morphology of the Genera|url=https://books.google.com/books?id=xhLJvNa3hw0C|access-date=13 November 2013|year=1990|publisher=Cambridge University Press|isbn=978-0-521-36318-1|archive-date=24 May 2021|archive-url=https://web.archive.org/web/20210524082251/https://books.google.com/books?id=xhLJvNa3hw0C|url-status=live}}{{page needed|date=March 2017}}</ref><ref name="Canter-Lund-1995">Canter-Lund, H. and Lund, J. W. G. (1995). ''Freshwater Algae: Their microscopic world explained'', Biopress Limited. {{ISBN|0-948737-25-5}}.{{page needed|date=March 2017}}</ref><ref>{{cite journal |doi=10.1007/BF00940439 |jstor=23675282 |title=The species concept in diatoms: Evidence for morphologically distinct, sympatric gamodemes in four epipelic species |journal=Plant Systematics and Evolution |volume=164 |issue=1/4 |pages=215–37 |year=2005 |last1=Mann |first1=David G. |s2cid=37684109 }}</ref>). Around 1,000–1,300 diatom genera have been described, both extant and fossil,<ref>{{cite journal |doi= 10.1080/0269249X.1999.9705462|title=Catalogue of the Diatom Genera |journal=Diatom Research |volume=14 |issue=1 |pages=1–190 |year=1999 |last1=Fourtanier |first1=Elisabeth |last2=Kociolek |first2=J. Patrick|bibcode=1999DiaRe..14....1F }}</ref><ref>The [[World Register of Marine Species]] lists 1,356 diatom genus names from all habitats as at July 2020, of which 1,248 are "accepted".</ref> of which some 250–300 exist only as fossils.<ref>Queries to the World Register of Marine Species, July 2020, return 299 "fossil only" genus names, of which 285 are "accepted".</ref>

===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]] and [[Pennales]]). 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]] 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]], 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]]'', which is an anomalous genus. Discussion of the relative merits of these conflicting schemes continues by the various parties involved.<ref>{{cite journal |doi=10.5091/plecevo.2010.418 |title=The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny |journal=European Journal of Phycology |volume=4 |issue=3 |pages=277–290 |year=2009 |last1=Theriot |first1=Edward C. |last2=Cannone |first2=Jamie J. |last3=Gutell |first3=Robin R. |last4=Alverson |first4=Andrew J.|pmid=20224747 |pmc=2835975 }}</ref><ref>{{cite journal |doi=10.1080/09670260902749159 |title=A preliminary multigene phylogeny of the diatoms (Bacillariophyta): challenges for future research |journal=Plant Ecology and Evolution |volume=143 |issue=3 |year=2010 |last1=Theriot |first1=Edward C. |last2=Ashworth |first2=Matt |last3=Ruck |first3=Elizabeth |last4=Nakov |first4=Teofil |last5=Jansen |first5=Robert K. |pages=277–290 |pmid=20224747 |pmc=2835975 |doi-access=free }}</ref><ref>{{cite journal |doi=10.1093/molbev/msx268 |title=Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta) |journal=Molecular Biology and Evolution |volume=35 |issue=1 |pages=80–93 |year=2018 |last1=Parks |first1=Matthew B. |last2=Wickett |first2=Norman J. |last3=Alverson |first3=Andrew J. |pmid=29040712 |pmc=5850769 |doi-access=free }}</ref><ref>{{cite journal |title=Review of the phylogenetic reconstruction of the diatoms using molecular tools with an analysis of a seven gene data set using multiple outgroups and morphological data for a total evidence approach |journal=Phycologia |volume=in press |year=2020 |last1=Medlin |first1=L.K. |last2=Desdevises |first2=Y. |url=http://plymsea.ac.uk/id/eprint/8938/1/PH20-10_R1.pdf |access-date=20 July 2020 |archive-date=20 July 2020 |archive-url=https://web.archive.org/web/20200720012627/http://plymsea.ac.uk/id/eprint/8938/1/PH20-10_R1.pdf |url-status=live }}</ref>

====Adl ''et al.'', 2019 treatment====
In 2019, Adl ''et al.''<ref name="Adl-2018">{{Cite journal |last1=Adl |first1=Sina M. |last2=Bass |first2=David |last3=Lane|first3=Christopher E. |last4=Lukeš |first4=Julius |last5=Schoch |first5=Conrad L. |last6=Smirnov |first6=Alexey |last7=Agatha |first7=Sabine |last8=Berney |first8=Cedric |last9=Brown |first9=Matthew W. | display-authors = 6 | date=2018-09-26 |title=Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes|journal=Journal of Eukaryotic Microbiology |volume=66 |issue=1 |pages=4–119 |doi=10.1111/jeu.12691|pmid=30257078 |pmc=6492006 }}</ref> 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 [[Clade|clades]] appear at a high classification level (and the higher level classification is rather flat)." This classification accepts the Mediophyceae of Medlin and co-workers and introduces new clades for a number of otherwise isolated genera.
* [[Ochrophyte|Ochrophyta]] Cavalier-Smith 1986, emend. Cavalier-Smith & Chao 1996 (ochrophytes)
** [[Diatomista]] Derelle et al. 2016, emend. Cavalier-Smith 2017 (diatoms plus a subset of other ochrophyte groups)
*** '''Diatomeae''' Dumortier 1821 [= [[Bacillariophyta]] Haeckel 1878] (diatoms)
**** [[Leptocylindrophytina]] D.G. Mann in Adl et al. 2019
***** [[Leptocylindrophyceae]] D.G. Mann in Adl et al. 2019 (''[[Leptocylindrus]]'', ''[[Tenuicylindrus]]'')
***** [[Corethrophyceae]] D.G. Mann in Adl et al. 2019 (''[[Corethron]]'')
**** [[Ellerbeckia|Ellerbeckiophytina]] D.G. Mann in Adl et al. 2019 (''[[Ellerbeckia]]'')
**** [[Probosciophytina]] D.G. Mann in Adl et al. 2019 (''[[Proboscia]]'')
**** [[Melosirophytina]] D.G. Mann in Adl et al. 2019 (''[[Aulacoseira]]'', ''[[Melosira]]'', ''[[Hyalodiscus]]'', ''[[Stephanopyxis]]'', ''[[Paralia (diatom genus)|Paralia]]'', ''[[Endictya]]'')
**** [[Coscinodiscophytina]] Medlin & Kaczmarska 2004, emend. (''[[Actinoptychus]]'', ''[[Coscinodiscus]]'', ''[[Actinocyclus]]'', ''[[Asteromphalus]]'', ''[[Aulacodiscus]]'', ''[[Stellarima]]'')
**** [[Rhizosoleniophytina]] D.G. Mann in Adl et al. 2019 (''[[Guinardia]]'', ''[[Rhizosolenia]]'', ''[[Pseudosolenia]]'')
**** [[Arachnoidiscophytina]] D.G. Mann in Adl et al. 2019 (''[[Arachnoidiscus]]'')
**** [[Bacillariophytina]] Medlin & Kaczmarska 2004, emend.
***** [[Mediophyceae]] Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
****** [[Chaetocerotophycidae]] Round & R.M. Crawford in Round et al. 1990, emend.
****** [[Lithodesmiophycidae]] Round & R.M. Crawford in Round et al. 1990, emend.
****** [[Thalassiosirophycidae]] Round & R.M. Crawford in Round et al. 1990
****** [[Cymatosirophycidae]] Round & R.M. Crawford in Round et al. 1990
****** [[Odontellophycidae]] D.G. Mann in Adl et al. 2019
****** [[Chrysanthemodiscophycidae]] D.G. Mann in Adl et al. 2019
***** [[Biddulphiophyceae]] D.G. Mann in Adl et al. 2019
****** [[Biddulphiophycidae]] Round and R.M. Crawford in Round et al. 1990, emend.
****** ''[[Attheya]]''
***** [[Bacillariophyceae]] Haeckel 1878, emend.
****** [[Striatellaceae]]
****** [[Urneidophycidae]] Medlin 2016
****** [[Fragilariophycidae]] Round in Round, Crawford & Mann 1990, emend.
****** [[Bacillariophycidae]] D.G. Mann in Round, Crawford & Mann 1990, emend.

See [[taxonomy of diatoms]] for more details.

== Evolution and fossil record ==
=== Origin ===
Heterokont chloroplasts appear to derive 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 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]] (~185 [[Mega-annum|Ma ago]]),<ref name="Kooistra-1996">{{cite journal |doi=10.1006/mpev.1996.0088 |pmid=8975694 |title=Evolution of the Diatoms (Bacillariophyta) |journal=Molecular Phylogenetics and Evolution |volume=6 |issue=3 |pages=391–407 |year=1996 |last1=Kooistra |first1=Wiebe H.C.F. |last2=Medlin |first2=Linda K. }}</ref> although the [[molecular clock]]<ref name="Kooistra-1996" /> and [[sedimentary rock|sedimentary]]<ref name="Schieber-2000">{{cite journal |doi=10.1038/35023143 |pmid=10984049 |year=2000 |last1=Schieber |first1=Jürgen |title=Diagenetic origin of quartz silt in mudstones and implications for silica cycling |journal=Nature |volume=406 |issue=6799 |pages=981–5 |last2=Krinsley |first2=Dave |last3=Riciputi |first3=Lee |bibcode=2000Natur.406..981S |s2cid=4417951 }}</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|niches]] were opened.<ref name="Medlin-1997">{{cite journal |hdl=10013/epic.12689 | 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? | journal=Nova Hedwigia | volume=65 | issue=1–4 | pages=1–11 | doi=10.1127/nova.hedwigia/65/1997/1 | bibcode=1997NovaH..65....1M }}</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="Raven-2004">{{cite journal |doi=10.1111/j.1469-8137.2004.01022.x |jstor=1514475 |title=The evolution of silicification in diatoms: Inescapable sinking and sinking as escape? |journal=New Phytologist |volume=162 |issue=1 |pages=45–61 |year=2004 |last1=Raven |first1=J. A. |last2=Waite |first2=A. M. |doi-access=free |bibcode=2004NewPh.162...45R }}</ref> 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]], and with some rocks such as [[diatomaceous earth]], being composed almost entirely of them.

===Relation to grasslands ===
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 promoted the diatoms during the Cenozoic era.<ref>{{cite journal |doi=10.1126/science.1095964 |pmid=15256663 |title=The Evolution of Modern Eukaryotic Phytoplankton |journal=Science |volume=305 |issue=5682 |pages=354–60 |year=2004 |last1=Falkowski |first1=P. G. |last2=Katz |first2=Miriam E. |last3=Knoll |first3=Andrew H. |last4=Quigg |first4=Antonietta |last5=Raven |first5=John A. |last6=Schofield |first6=Oscar |last7=Taylor |first7=F. J. R. |bibcode=2004Sci...305..354F |citeseerx=10.1.1.598.7930 |s2cid=451773 }}</ref><ref>{{cite journal |doi=10.2110/palo.2003.p03-108 |jstor=27670327 |title=Impact of Grassland Radiation on the Nonmarine Silica Cycle and Miocene Diatomite |journal=PALAIOS |volume=20 |issue=2 |pages=198–206 |year=2005 |last1=Kidder |first1=D. L. |last2=Gierlowski-Kordesch |first2=E. H. |bibcode=2005Palai..20..198K |s2cid=140584104 }}</ref> 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.<ref name="Lazarus-2014">{{cite journal |doi=10.1371/journal.pone.0084857 |pmid=24465441 |pmc=3898954 |title=Cenozoic Planktonic Marine Diatom Diversity and Correlation to Climate Change |journal=PLOS ONE |volume=9 |issue=1 |article-number=e84857 |year=2014 |last1=Lazarus |first1=David |last2=Barron |first2=John |last3=Renaudie |first3=Johan |last4=Diver |first4=Patrick |last5=Türke |first5=Andreas |bibcode=2014PLoSO...984857L |doi-access=free }}</ref>

===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,<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="Lazarus-2014" />

=== Method of investigation ===
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="Scherer-2007">{{cite journal |last1=Scherer |first1=R. P. |last2=Gladenkov |first2=A. Yu. |last3=Barron |first3=J. A. |year=2007 |title=Methods and applications of Cenozoic marine diatom biostratigraphy |journal=Paleontological Society Papers |volume=13 |pages=61–83 |doi=10.1017/S1089332600001467 }}</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.

Diatoms preserved in lake sediments are widely used for [[Paleoecology|paleoenvironmental reconstructions]] of [[Quaternary]] climate, especially for closed-basin lakes which experience fluctuations in water depth and salinity.

===Isotope records===
[[File:Triceratium morlandii var. morlandii.jpg|thumb| {{center|Intricate silicate (glass) shell, 32-40 million years old, of a diatom [[microfossil]]}}]]
{{further|microfossils}}

When diatoms die their shells ([[frustule]]s) can settle on the [[seafloor]] and become [[microfossil]]s. Over time, these microfossils become buried as [[opal]] deposits in the [[marine sediment]]. [[Paleoclimatology]] is the study of past climates. [[Proxy (climate)|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]] refer to preserved or fossilized physical markers which serve as substitutes for direct meteorological or ocean measurements.<ref>{{Cite web|title=What Are "Proxy" Data? {{!}} National Centers for Environmental Information (NCEI) formerly known as National Climatic Data Center (NCDC)|url=https://www.ncdc.noaa.gov/news/what-are-proxy-data|access-date=2020-10-20|website=www.ncdc.noaa.gov|archive-date=8 March 2020|archive-url=https://web.archive.org/web/20200308170642/https://www.ncdc.noaa.gov/news/what-are-proxy-data|url-status=live}}</ref> An example of proxies is the use of diatom [[marine isotope stage|isotope records]] of [[δ13C]], [[δ18O]], [[Isotopes of silicon|δ30Si]] (δ13C<sub>diatom</sub>, δ18O<sub>diatom</sub>, and δ30Si<sub>diatom</sub>). In 2015, Swann and Snelling used these isotope records to document historic changes in the photic zone conditions of the north-west [[Pacific Ocean]], including nutrient supply and the efficiency of the soft-tissue [[biological pump]], from the modern day back to [[Marine Isotope Stage 5#Marine Isotope Stage (MIS) 5e|marine isotope stage 5e]], which coincides with the [[Eemian|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]].<ref name="Swann-2015">{{cite journal | last1=Swann | first1=G. E. A. | last2=Snelling | first2=A. M. | title=Photic zone changes in the north-west Pacific Ocean from MIS 4–5e | journal=Climate of the Past | publisher=Copernicus GmbH | volume=11 | issue=1 | date=2015-01-06 | issn=1814-9332 | doi=10.5194/cp-11-15-2015 | pages=15–25| bibcode=2015CliPa..11...15S | doi-access=free }} [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/3.0/ Creative Commons Attribution 3.0 International License] {{Webarchive|url=https://web.archive.org/web/20110223101209/http://creativecommons.org//licenses//by//3.0// |date=23 February 2011 }}.</ref>

<gallery mode="packed" style="float:left" heights="220px">
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
</gallery>
{{clear}}

The initial development of the halocline and [[Stratification (water)|stratified water column]] has been attributed to the onset of major [[Würm glaciation|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 temperature]]s.<ref>{{cite journal | last1=Sigman | first1=Daniel M. | last2=Jaccard | first2=Samuel L. | last3=Haug | first3=Gerald H. | title=Polar ocean stratification in a cold climate | journal=Nature | publisher=Springer Science and Business Media LLC | volume=428 | issue=6978 | year=2004 | issn=0028-0836 | doi=10.1038/nature02357 | pages=59–63 | pmid=14999278 | bibcode=2004Natur.428...59S | s2cid=4329978 | url=https://gfzpublic.gfz-potsdam.de/pubman/item/item_230448 | access-date=15 December 2021 | archive-date=19 February 2022 | archive-url=https://web.archive.org/web/20220219150343/https://gfzpublic.gfz-potsdam.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_230448 | url-status=live }}</ref><ref name="Haug-2005">{{cite journal | last1=Haug | first1=Gerald H. | last2=Ganopolski | first2=Andrey | last3=Sigman | first3=Daniel M. | last4=Rosell-Mele | first4=Antoni | last5=Swann | first5=George E. A. | last6=Tiedemann | first6=Ralf | last7=Jaccard | first7=Samuel L. | last8=Bollmann | first8=Jörg | last9=Maslin | first9=Mark A. | last10=Leng | first10=Melanie J. | last11=Eglinton | first11=Geoffrey | display-authors = 6 | title=North Pacific seasonality and the glaciation of North America 2.7 million years ago | journal=Nature | publisher=Springer Science and Business Media LLC | volume=433 | issue=7028 | year=2005 | issn=0028-0836 | doi=10.1038/nature03332 | pages=821–825 | pmid=15729332 | bibcode=2005Natur.433..821H | s2cid=24116155 | url=https://gfzpublic.gfz-potsdam.de/pubman/item/item_231798 | access-date=15 December 2021 | archive-date=19 February 2022 | archive-url=https://web.archive.org/web/20220219150343/https://gfzpublic.gfz-potsdam.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_231798 | url-status=live }}</ref><ref>{{cite journal | last1=Swann | first1=George E. A. | last2=Maslin | first2=Mark A. | last3=Leng | first3=Melanie J. | last4=Sloane | first4=Hilary J. | last5=Haug | first5=Gerald H. | title=Diatom δ18O evidence for the development of the modern halocline system in the subarctic northwest Pacific at the onset of major Northern Hemisphere glaciation | journal=Paleoceanography | publisher=American Geophysical Union (AGU) | volume=21 | issue=1 | date=2006-02-24 | issn=0883-8305 | doi=10.1029/2005pa001147 | pages=n/a| bibcode=2006PalOc..21.1009S | url=http://eprints.nottingham.ac.uk/id/eprint/2009 | doi-access=free }}</ref><ref name="Nie-2008">{{cite journal | last1=Nie | first1=Junsheng | last2=King | first2=John | last3=Liu | first3=Zhengyu | last4=Clemens | first4=Steve | last5=Prell | first5=Warren | last6=Fang | first6=Xiaomin | title=Surface-water freshening: A cause for the onset of North Pacific stratification from 2.75 Ma onward? | journal=Global and Planetary Change | publisher=Elsevier BV | volume=64 | issue=1–2 | year=2008 | issn=0921-8181 | doi=10.1016/j.gloplacha.2008.08.003 | pages=49–52| bibcode=2008GPC....64...49N }}</ref> 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.<ref name="Haug-2005" /> While the halocline appears to have prevailed through the [[late Pliocene]] and [[Gelasian|early Quaternary]] [[glacial cycle|glacial–interglacial cycles]],<ref>{{cite journal | last=Swann | first=George E.A. | title=Salinity changes in the North West Pacific Ocean during the late Pliocene/early Quaternary from 2.73Ma to 2.52Ma | journal=Earth and Planetary Science Letters | publisher=Elsevier BV | volume=297 | issue=1–2 | year=2010 | issn=0012-821X | doi=10.1016/j.epsl.2010.06.035 | pages=332–338 | bibcode=2010E&PSL.297..332S | url=http://nora.nerc.ac.uk/id/eprint/11147/1/swann_et_al_2010.pdf | access-date=15 December 2021 | archive-date=19 July 2018 | archive-url=https://web.archive.org/web/20180719072730/http://nora.nerc.ac.uk/id/eprint/11147/1/swann_et_al_2010.pdf | url-status=live }}</ref> 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.<ref>{{cite journal | last1=Sarnthein | first1=M. | last2=Gebhardt | first2=H. | last3=Kiefer | first3=T. | last4=Kucera | first4=M. | last5=Cook | first5=M. | last6=Erlenkeuser | first6=H. | title=Mid Holocene origin of the sea-surface salinity low in the subarctic North Pacific | journal=Quaternary Science Reviews | publisher=Elsevier BV | volume=23 | issue=20–22 | year=2004 | issn=0277-3791 | doi=10.1016/j.quascirev.2004.08.008 | pages=2089–2099| bibcode=2004QSRv...23.2089S }}</ref><ref>{{cite journal | last1=Jaccard | first1=S.L. | last2=Galbraith | first2=E.D. | last3=Sigman | first3=D.M. | last4=Haug | first4=G.H. | title=A pervasive link between Antarctic ice core and subarctic Pacific sediment records over the past 800kyrs | journal=Quaternary Science Reviews | publisher=Elsevier BV | volume=29 | issue=1–2 | year=2010 | issn=0277-3791 | doi=10.1016/j.quascirev.2009.10.007 | pages=206–212| bibcode=2010QSRv...29..206J }}</ref><ref>{{cite journal | last1=Galbraith | first1=Eric D. | last2=Kienast | first2=Markus | last3=Jaccard | first3=Samuel L. | last4=Pedersen | first4=Thomas F. | last5=Brunelle | first5=Brigitte G. | last6=Sigman | first6=Daniel M. | last7=Kiefer | first7=Thorsten | title=Consistent relationship between global climate and surface nitrate utilization in the western subarctic Pacific throughout the last 500 ka | journal=Paleoceanography | publisher=American Geophysical Union (AGU) | volume=23 | issue=2 | date=2008-05-23 | issn=0883-8305 | doi=10.1029/2007pa001518 | pages=n/a | bibcode=2008PalOc..23.2212G | s2cid=4082469 | url=https://archimer.ifremer.fr/doc/00237/34840/33281.pdf | access-date=15 December 2021 | archive-date=15 July 2021 | archive-url=https://web.archive.org/web/20210715195452/https://archimer.ifremer.fr/doc/00237/34840/33281.pdf | url-status=live }}</ref><ref>{{cite journal | last1=Brunelle | first1=Brigitte G. | last2=Sigman | first2=Daniel M. | last3=Jaccard | first3=Samuel L. | last4=Keigwin | first4=Lloyd D. | last5=Plessen | first5=Birgit | last6=Schettler | first6=Georg | last7=Cook | first7=Mea S. | last8=Haug | first8=Gerald H. | title=Glacial/interglacial changes in nutrient supply and stratification in the western subarctic North Pacific since the penultimate glacial maximum | journal=Quaternary Science Reviews | publisher=Elsevier BV | volume=29 | issue=19–20 | year=2010 | issn=0277-3791 | doi=10.1016/j.quascirev.2010.03.010 | pages=2579–2590| bibcode=2010QSRv...29.2579B }}</ref><ref>{{cite journal | last1=Kohfeld | first1=Karen E. | last2=Chase | first2=Zanna | title=Controls on deglacial changes in biogenic fluxes in the North Pacific Ocean | journal=Quaternary Science Reviews | publisher=Elsevier BV | volume=30 | issue=23–24 | year=2011 | issn=0277-3791 | doi=10.1016/j.quascirev.2011.08.007 | pages=3350–3363| bibcode=2011QSRv...30.3350K }}</ref><ref name="Swann-2015" />

===Diversification===
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="Harwood-2007">{{cite journal |last1=Harwood |first1=D. M. |last2=Nikolaev |first2=V. A. |last3=Winter |first3=D. M. |year=2007 |title=Cretaceous record of diatom evolution, radiation, and expansion |journal=Paleontological Society Papers |volume=13 |pages=33–59 |doi=10.1017/S1089332600001455 }}</ref>

===Turnover===
Although no mass extinctions of marine diatoms have been observed during the [[Cenozoic]], times of relatively rapid evolutionary turnover in marine diatom species assemblages occurred near the [[Paleocene]]–[[Eocene]] boundary,<ref name="Strelnikova-1990">{{cite book |last=Strelnikova |first=N. I. |year=1990 |chapter=Evolution of diatoms during the Cretaceous and Paleogene periods |editor-last=Simola |editor-first=H. |title=Proceedings of the Tenth International Diatom Symposium |publisher=Koeltz Scientific Books |location=Koenigstein |pages=195–204 |isbn=3-87429-307-6 }}</ref> and at the [[Eocene]]–[[Oligocene]] boundary.<ref name="Baldauf-1993">{{cite book |last=Baldauf |first=J. G. |year=1993 |contribution=Middle Eocene through early Miocene diatom floral turnover |editor-last=Prothero |editor-first=D. |editor2-last=Berggren |editor2-first=W. H. |title=Eocene-Oligocene climatic and biotic evolution |publisher=Princeton University Press |location=Princeton |pages=310–326 |isbn=0-691-02542-8 }}</ref> Further turnover of assemblages took place at various times between the middle [[Miocene]] and late [[Pliocene]],<ref name="Barron-2003">{{cite journal |last=Barron |first=J. A. |year=2003 |title=Appearance and extinction of planktonic diatoms during the past 18&nbsp;m.y. in the Pacific and Southern oceans |journal=Diatom Research |volume=18 |pages=203–224 |doi=10.1080/0269249x.2003.9705588 |s2cid=84781882 }}</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="Scherer-2007" /> 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 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]].

==Genetics==
[[File:Phaeodactylum tricornutum.png|thumb|210px| {{center|''[[Phaeodactylum tricornutum]]'' is widely used as a [[model organism]]}}]]

=== Expressed sequence tagging ===
In 2002, the first insights into the properties of the ''[[Phaeodactylum tricornutum]]'' gene repertoire were described using 1,000 [[expressed sequence tag]]s (ESTs).<ref name="Scala-2002">{{cite journal |doi=10.1104/pp.010713 |pmid=12114555 |pmc=166495 |title=Genome Properties of the Diatom Phaeodactylum tricornutum |journal=Plant Physiology |volume=129 |issue=3 |pages=993–1002 |year=2002 |last1=Scala |first1=S. |last2=Carels |first2=N |last3=Falciatore |first3=A |last4=Chiusano |first4=M. L. |last5=Bowler |first5=C }}</ref> Subsequently, the number of ESTs was extended to 12,000 and the diatom EST database was constructed for functional analyses.<ref name="Maheswari-2004">{{cite journal |doi=10.1093/nar/gki121 |pmid=15608213 |pmc=540075 |title=The Diatom EST Database |journal=Nucleic Acids Research |volume=33 |issue=Database issue |pages=D344–7 |year=2004 |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. }}</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="Montsant-2005">{{cite journal |doi=10.1104/pp.104.052829 |pmid=15665249 |pmc=1065351 |title=Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum |journal=Plant Physiology |volume=137 |issue=2 |pages=500–13 |year=2005 |last1=Montsant |first1=A. |last2=Jabbari |first2=K |last3=Maheswari |first3=U |last4=Bowler |first4=C }}</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.<ref>{{cite journal |doi=10.1093/nar/gkn905 |pmid=19029140 |pmc=2686495 |title=Update of the Diatom EST Database: A new tool for digital transcriptomics |journal=Nucleic Acids Research |volume=37 |issue=Database issue |pages=D1001–5 |year=2009 |last1=Maheswari |first1=U. |last2=Mock |first2=T. |last3=Armbrust |first3=E. V. |last4=Bowler |first4=C. }}</ref>

=== Genome sequencing ===
[[File:Thalassiosira pseudonana.jpg|thumb|210px| {{center|''[[Thalassiosira pseudonana]]'' was the first eukaryotic marine phytoplankton to  have its genome sequenced}}]]

In 2004, the entire [[genome]] of the centric diatom, ''[[Thalassiosira pseudonana]]'' (32.4 Mb) was sequenced,<ref name="Armbrust-2004a">{{cite journal |doi=10.1126/science.1101156 |pmid=15459382 |title=The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism |journal=Science |volume=306 |issue=5693 |pages=79–86 |year=2004 |last1=Armbrust |first1=E. V. |last2=Berges |first2=John A. |last3=Bowler |first3=Chris |last4=Green |first4=Beverley R. |last5=Martinez |first5=Diego |last6=Putnam |first6=Nicholas H. |last7=Zhou |first7=Shiguo |last8=Allen |first8=Andrew E. |last9=Apt |first9=Kirk E. |last10=Bechner |first10=Michael |last11=Brzezinski |first11=Mark A. |last12=Chaal |first12=Balbir K. |last13=Chiovitti |first13=Anthony |last14=Davis |first14=Aubrey K. |last15=Demarest |first15=Mark S. |last16=Detter |first16=J. Chris |last17=Glavina |first17=Tijana |last18=Goodstein |first18=David |last19=Hadi |first19=Masood Z. |last20=Hellsten |first20=Uffe |last21=Hildebrand |first21=Mark |last22=Jenkins |first22=Bethany D. |last23=Jurka |first23=Jerzy |last24=Kapitonov |first24=Vladimir V. |last25=Kröger |first25=Nils |last26=Lau |first26=Winnie W. Y. |last27=Lane |first27=Todd W. |last28=Larimer |first28=Frank W. |last29=Lippmeier |first29=J. Casey |last30=Lucas |first30=Susan | display-authors = 6 | bibcode=2004Sci...306...79A |citeseerx=10.1.1.690.4884 |s2cid=8593895 }}</ref> followed in 2008 with the sequencing of the pennate diatom, ''[[Phaeodactylum tricornutum]]'' (27.4 Mb).<ref name="Bowler-2008">{{cite journal |doi=10.1038/nature07410 |pmid=18923393 |title=The Phaeodactylum genome reveals the evolutionary history of diatom genomes |journal=Nature |volume=456 |issue=7219 |pages=239–244 |year=2008 |last1=Bowler |first1=Chris |last2=Allen |first2=Andrew E. |last3=Badger |first3=Jonathan H. |last4=Grimwood |first4=Jane |last5=Jabbari |first5=Kamel |last6=Kuo |first6=Alan |last7=Maheswari |first7=Uma |last8=Martens |first8=Cindy |last9=Maumus |first9=Florian |last10=Otillar |first10=Robert P. |last11=Rayko |first11=Edda |last12=Salamov |first12=Asaf |last13=Vandepoele |first13=Klaas |last14=Beszteri |first14=Bank |last15=Gruber |first15=Ansgar |last16=Heijde |first16=Marc |last17=Katinka |first17=Michael |last18=Mock |first18=Thomas |last19=Valentin |first19=Klaus |last20=Verret |first20=Fréderic |last21=Berges |first21=John A. |last22=Brownlee |first22=Colin |last23=Cadoret |first23=Jean-Paul |last24=Chiovitti |first24=Anthony |last25=Choi |first25=Chang Jae |last26=Coesel |first26=Sacha |last27=De Martino |first27=Alessandra |last28=Detter |first28=J. Chris |last29=Durkin |first29=Colleen |last30=Falciatore |first30=Angela |display-authors = 6 | bibcode=2008Natur.456..239B |s2cid=4415177 |doi-access=free }}</ref> 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.<ref name="Bowler-2008" /><ref>{{cite journal |doi=10.1093/molbev/msm048 |pmid=17350938 |title=A Very High Fraction of Unique Intron Positions in the Intron-Rich Diatom Thalassiosira pseudonana Indicates Widespread Intron Gain |journal=Molecular Biology and Evolution |volume=24 |issue=7 |pages=1447–57 |year=2007 |last1=Roy |first1=S. W. |last2=Penny |first2=D. |doi-access=free }}</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="Bowler-2008" /> [[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="Maumus-2009">{{cite journal |doi=10.1186/1471-2164-10-624 |pmid=20028555 |pmc=2806351 |title=Potential impact of stress activated retrotransposons on genome evolution in a marine diatom |journal=BMC Genomics |volume=10 |page=624 |year=2009 |last1=Maumus |first1=Florian |last2=Allen |first2=Andrew E |last3=Mhiri |first3=Corinne |last4=Hu |first4=Hanhua |last5=Jabbari |first5=Kamel |last6=Vardi |first6=Assaf |last7=Grandbastien |first7=Marie-Angèle |last8=Bowler |first8=Chris |doi-access=free }}</ref>

===Endosymbiotic gene transfer===
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="Armbrust-2004a" /> More recent [[phylogenomics|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 |doi=10.1126/science.1172983 |pmid=19556510 |title=Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms |journal=Science |volume=324 |issue=5935 |pages=1724–6 |year=2009 |last1=Moustafa |first1=A. |last2=Beszteri |first2=B. |last3=Maier |first3=U. G. |last4=Bowler |first4=C. |last5=Valentin |first5=K. |last6=Bhattacharya |first6=D. |bibcode=2009Sci...324.1724M |s2cid=11408339 |url=http://epic.awi.de/20816/1/Mou2009a.pdf |access-date=13 January 2019 |archive-url=https://web.archive.org/web/20140421015051/http://epic.awi.de/20816/1/Mou2009a.pdf |archive-date=21 April 2014 }}</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.

===Horizontal gene transfer===
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="Bowler-2008" />

===Genetic engineering===
To understand the biological mechanisms which underlie the great importance of diatoms in geochemical cycles, scientists have used the ''[[Phaeodactylum tricornutum]]'' and ''[[Thalassiosira]] spp.'' species as model organisms since the 90's.<ref name="Kroth-2018">{{cite journal |display-authors=2 |last1=Kroth |first1=Peter G. |last2=Bones |first2=Atle M. |last3=Daboussi |first3=Fayza |title=Genome editing in diatoms: achievements and goals |journal=Plant Cell Reports |date=Oct 2018 |volume=37 |issue=10 |pages=1401–1408 |doi=10.1007/s00299-018-2334-1 |pmid=30167805 |bibcode=2018PCelR..37.1401K |s2cid=52133809 |url=http://nbn-resolving.de/urn:nbn:de:bsz:352-2-1lxrzq3xck4wo8 |access-date=20 May 2021 |archive-date=19 February 2022 |archive-url=https://web.archive.org/web/20220219150345/https://kops.uni-konstanz.de/handle/123456789/44586 |url-status=live |hdl=11250/2590892 |hdl-access=free }}</ref>
Few molecular biology tools are currently available to generate mutants or transgenic lines : [[plasmids]] containing transgenes are inserted into the cells using the [[biolistic]] method<ref name="Falciatore-2015">{{cite journal |display-authors=2 |last1=Falciatore |first1=Angela |last2=Casotti |first2=Raffaella |last3=Leblanc |first3=Catherine |last4=Abrascia |first4=Chiara |last5=Bowler |first5=Chris |title=Transformation of Nonselectablporter Genes in Marine Diatomse Re |journal=Marine Biotechnology |date=May 2015 |volume=1 |issue=3 |pages=239–251 |doi=10.1007/PL00011773|pmid=10383998 |s2cid=22267097 }}</ref> or transkingdom [[bacterial conjugation]]<ref name="Karas-2015">{{cite journal |last1=Karas |first1=Bogumil J. |last2=Diner |first2=Rachel E. |last3=Lefebvre |first3=Stephane C. |last4=McQuaid |first4=Jeff |last5=Phillips |first5=Alex P. R. |last6=Noddings |first6=Chari M. |last7=Brunson |first7=John K. |last8=Valas |first8=Ruben E. |last9=Deerinck |first9=Thomas J. |last10=Jablanovic |first10=Jelena |last11=Gillard |first11=Jeroen T. F. |last12=Beeri |first12=Karen |last13=Ellisman |first13=Mark H. |last14=Glass |first14=John I. |last15=Hutchison Iii |first15=Clyde A. |last16=Smith |first16=Hamilton O. |last17=Venter |first17=J. Craig |last18=Allen |first18=Andrew E. |last19=Dupont |first19=Christopher L. |last20=Weyman |first20=Philip D. | display-authors = 6 | title=Designer diatom episomes delivered by bacterial conjugation |journal=Nature Communications |date=21 April 2015 |volume=6 |issue=1 |page=6925 |doi=10.1038/ncomms7925 |pmid=25897682 |pmc=4411287 |bibcode=2015NatCo...6.6925K |language=en |issn=2041-1723|doi-access=free }}</ref> (with 10<sup>−6</sup> and 10<sup>−4</sup> yield respectively<ref name="Falciatore-2015" /><ref name="Karas-2015" />), and other classical transfection methods such as [[electroporation]] or use of [[Polyethylene glycol|PEG]] have been reported to provide results with lower efficiencies.<ref name="Karas-2015" />

Transfected plasmids can be either randomly integrated into the diatom's chromosomes or maintained as stable circular [[episomes]] (thanks to the CEN6-ARSH4-HIS3 yeast centromeric sequence<ref name="Karas-2015" />). The phleomycin/[[Zeocin|zeocin resistance gene Sh Ble]] is commonly used as a selection marker,<ref name="Kroth-2018" /><ref name="Slattery-2018">{{cite journal |last1=Slattery |first1=Samuel S. |last2=Diamond |first2=Andrew |last3=Wang |first3=Helen |last4=Therrien |first4=Jasmine A. |last5=Lant |first5=Jeremy T. |last6=Jazey |first6=Teah |last7=Lee |first7=Kyle |last8=Klassen |first8=Zachary |last9=Desgagné-Penix |first9=Isabel |last10=Karas |first10=Bogumil J. |last11=Edgell |first11=David R. | display-authors = 6 | title=An Expanded Plasmid-Based Genetic Toolbox Enables Cas9 Genome Editing and Stable Maintenance of Synthetic Pathways in Phaeodactylum tricornutum |journal=ACS Synthetic Biology |date=16 February 2018 |volume=7 |issue=2 |pages=328–338 |doi=10.1021/acssynbio.7b00191|pmid=29298053 }}</ref> and various transgenes have been successfully introduced and expressed in diatoms with stable transmissions through generations,<ref name="Karas-2015" /><ref name="Slattery-2018" /> or with the possibility to remove it.<ref name="Slattery-2018" />

Furthermore, these systems now allow the use of the [[CRISPR gene editing|CRISPR-Cas genome edition tool]], leading to a fast production of functional [[Gene knockout|knock-out mutants]]<ref name="Slattery-2018" /><ref name="Nymark-2016">{{cite journal |display-authors=2 |last1=Nymark |first1=Marianne |last2=Sharma |first2=Amit Kumar |last3=Sparstad |first3=Torfinn |last4=Bones |first4=Atle M. |last5=Winge |first5=Per |title=A CRISPR/Cas9 system adapted for gene editing in marine algae |journal=Scientific Reports |date=July 2016 |volume=6 |issue=1 |article-number=24951 |doi=10.1038/srep24951|pmid=27108533 |pmc=4842962 |bibcode=2016NatSR...624951N |doi-access=free }}</ref> and a more accurate comprehension of the diatoms' cellular processes.

==Human uses==
<gallery mode="packed" style="float:right" heights="200px">
File:Diatomaceous Earth BrightField.jpg| [[Diatomaceous earth]] consisting of centric (radially symmetric) and pennate (bilaterally symmetric) diatoms suspended in water.<br /><small>(click 3 times to fully enlarge)</small>
</gallery>

===Paleontology===
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]]).

===Industrial===
Diatoms, and their shells (frustules) as [[diatomite]] or [[diatomaceous earth]], 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.<ref>{{cite journal| pmc=5496942 | pmid=28725218 | doi=10.3389/fmicb.2017.01239 | volume=8 | title=All New Faces of Diatoms: Potential Source of Nanomaterials and Beyond | year=2017 | journal=Front Microbiol | page=1239 | last1=Mishra | first1=M | last2=Arukha | first2=AP | last3=Bashir | first3=T | last4=Yadav | first4=D | last5=Gbks | first5=Prasad| doi-access=free }}</ref>

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.<ref>{{cite journal |last1=Reka |first1=Arianit A. |last2=Pavlovski |first2=Blagoj |last3=Makreski |first3=Petre |title=New optimized method for low-temperature hydrothermal production of porous ceramics using diatomaceous earth |journal=Ceramics International |date=October 2017 |volume=43 |issue=15 |pages=12572–12578 |doi=10.1016/j.ceramint.2017.06.132 |url=https://www.researchgate.net/publication/317746441 |access-date=8 April 2020 |archive-date=19 February 2022 |archive-url=https://web.archive.org/web/20220219150340/https://www.researchgate.net/publication/317746441_New_optimized_method_for_low-temperature_hydrothermal_production_of_porous_ceramics_using_diatomaceous_earth |url-status=live }}</ref><ref>{{cite journal |last1=Reka |first1=Arianit |last2=Anovski |first2=Todor |last3=Bogoevski |first3=Slobodan |last4=Pavlovski |first4=Blagoj |last5=Boškovski |first5=Boško |title=Physical-chemical and mineralogical-petrographic examinations of diatomite from deposit near village of Rožden, Republic of Macedonia |journal=Geologica Macedonica |date=29 December 2014 |volume=28 |issue=2 |pages=121–126 |url=http://js.ugd.edu.mk/index.php/GEOLMAC/article/view/920 |language=en |issn=1857-8586 |access-date=8 April 2020 |archive-url=https://web.archive.org/web/20200418184959/http://js.ugd.edu.mk/index.php/GEOLMAC/article/view/920 |archive-date=18 April 2020 }}</ref><ref>{{cite journal |last1=Reka |first1=Arianit A. |last2=Pavlovski |first2=Blagoj |last3=Ademi |first3=Egzon |last4=Jashari |first4=Ahmed |last5=Boev |first5=Blazo |last6=Boev |first6=Ivan |last7=Makreski |first7=Petre |title=Effect Of Thermal Treatment Of Trepel At Temperature Range 800-1200˚C |journal=Open Chemistry |date=31 December 2019 |volume=17 |issue=1 |pages=1235–1243 |doi=10.1515/chem-2019-0132 |doi-access=free }}</ref>

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]].<ref name="Bradbury-2004">{{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 | doi-access=free }}</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 vehicles for [[drug delivery]]. With an appropriate [[artificial selection]] procedure, diatoms that produce valves of particular shapes and sizes might be evolved for cultivation in [[chemostat]] cultures to [[mass production|mass-produce]] nanoscale components.<ref name="Drum-2003">{{cite journal |doi=10.1016/S0167-7799(03)00169-0 |pmid=12902165 |title=Star Trek replicators and diatom nanotechnology |journal=Trends in Biotechnology |volume=21 |issue=8 |pages=325–8 |year=2003 |last1=Drum |first1=Ryan W. |last2=Gordon |first2=Richard }}</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 that diatoms normally use to create their cell walls.<ref>{{cite magazine | url=http://www.eetimes.com/showArticle.jhtml?articleID=216500176 | archive-url=https://archive.today/20120731133532/http://www.eetimes.com/showArticle.jhtml?articleID=216500176 | archive-date=31 July 2012 | title=Diatoms could triple solar cell efficiency | last=Johnson | first=R.C. | date=9 April 2009 | access-date=13 April 2009 | magazine=[[EE Times]] }}</ref> Diatom biofuel producing solar panels have also been proposed.<ref>{{cite journal |doi=10.1021/ie900044j |title=Milking Diatoms for Sustainable Energy: Biochemical Engineering versus Gasoline-Secreting Diatom Solar Panels |journal=Industrial & Engineering Chemistry Research |volume=48 |issue=19 |pages=8769–88 |year=2009 |last1=Ramachandra |first1=T. V. |last2=Mahapatra |first2=Durga Madhab |last3=b |first3=Karthick |last4=Gordon |first4=Richard }}</ref>
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<gallery mode="packed" style="float:left" heights="360px" caption="Supporting and regulating services provided by marine diatoms and some of their negative impacts">
File:Supporting and regulating services provided by marine diatoms.png|alt=CNN = cloud condensation nuclei, DMS = dimethylsulphide, DMSP = dimethylsulfoniopropionate, VOCs = volatile organic compounds, dashed arrow: negative effect, solid arrow: positive effects| <small>{{space|40}} CNN = [[cloud condensation nuclei]], DMS = [[dimethylsulphide]], DMSP = [[dimethylsulfoniopropionate]], VOCs = [[volatile organic compound]]s<br />{{space|50}}dashed arrow: negative effect, solid arrow: positive effects</small>
</gallery>
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=== Forensic ===
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]]. 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.<ref>{{cite journal |doi=10.1097/00000433-199109000-00009 |pmid=1750392 |title=Qualitative Diatom Analysis as a Tool to Diagnose Drowning |journal=The American Journal of Forensic Medicine and Pathology |volume=12 |issue=3 |pages=213–8 |year=1991 |last1=Auer |first1=Antti |s2cid=38370984 }}</ref>

==History of discovery==
[[File:Ränivetikas Tabellaria fenestrata.jpg|thumb| ''[[Tabellaria]]'' is a genus of freshwater diatoms, cuboid in shape with frustules (siliceous cell walls) attached at the corners so the colonies assume a zigzag shape.]]

The first illustrations of diatoms are found in an article from 1703 in Transactions of the Royal Society showing unmistakable drawings of ''Tabellaria''.<ref name="Karlusich-2020">{{Cite journal|last1=Pierella Karlusich|first1=Juan José|last2=Ibarbalz|first2=Federico M|last3=Bowler|first3=Chris|title=Exploration of marine phytoplankton: from their historical appreciation to the omics era|journal=Journal of Plankton Research|year=2020|volume=42|pages=595–612|doi=10.1093/plankt/fbaa049|doi-access=free|hdl=11336/143676|hdl-access=free}}</ref> Although the publication was authored by an unnamed English gentleman, there is recent evidence that he was Charles King of Staffordshire.<ref name="Karlusich-2020" /><ref>{{Cite journal|date=2019-08-01|title=Unmasking "The Eldest Son of The Father of Protozoology": Charles King|journal=Protist|language=en|volume=170|issue=4|pages=374–384|doi=10.1016/j.protis.2019.07.002|issn=1434-4610|last1=Dolan|first1=John R.|pmid=31479910|s2cid=201207778|doi-access=free}}</ref> The first formally identified diatom, the colonial ''Bacillaria paxillifera'', was discovered and described in 1783 by Danish naturalist [[Otto Friedrich Müller]].<ref name="Karlusich-2020" /> Like many others after him, he wrongly thought that it was an animal due to its ability to move. Even [[Charles Darwin]] 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 wrote, "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.<ref>{{Cite book|last=Darwin|first=Richard|title=On the Origin of Species by Means of Natural Selection: Or the Preservation of Favoured Races in the Struggle for Life|year=1866}}</ref>
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==Gallery==
<gallery mode="packed" widths="200px" heights="160px" style="float:left" caption="Scanning electron microscope images">
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''
</gallery>
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<gallery mode="packed" style="float:left" heights="170px">
File:Bacillaria paxillifera.jpg| Stand-alone cell of ''[[Bacillaria paxillifer]]''
File:Bacillaria paxillifer.tif| Colonial group of ''Bacillaria paxillifer''
</gallery>
{{ external media
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| video1 = [https://www.youtube.com/watch?v=Nysdq_plUTg&ab_channel=JourneytotheMicrocosmos Bacillaria: Distractingly Beautiful Crystal Colonies] – Journey to the Microcosmos:
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Three diatom species were sent to the [[International Space Station]], including the huge (6&nbsp;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 [[microfluidic]]s method.<ref>{{cite journal | last1=Mishra | first1=Meerambika | last2=Arukha | first2=Ananta P. | last3=Bashir | first3=Tufail | last4=Yadav | first4=Dhananjay | last5=Prasad | first5=G. B. K. S. | title=All New Faces of Diatoms: Potential Source of Nanomaterials and Beyond | journal=Frontiers in Microbiology | publisher=Frontiers Media SA | volume=8 | date=5 July 2017 | page=1239 | issn=1664-302X | doi=10.3389/fmicb.2017.01239| pmid=28725218 | pmc=5496942 | doi-access=free }} [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=16 October 2017 }}.</ref>

==See also==
<!-- Please respect alphabetical order -->
*[[Highly branched isoprenoid]], long-chain [[alkene]]s produced by a small number of marine diatoms

== Notes ==
{{notelist}}

==References==
{{Reflist}}

== External links ==
{{Wikispecies | Bacillariophyta | Diatoms}}
{{Commons category|Diatoms}}

* [http://www.biologie.ens.fr/diatomics/EST/ Diatom EST database], {{lang|fr|[[École Normale Supérieure]]|italic=no}}
* [http://planktonnet.awi.de/ Plankton*Net] {{Webarchive|url=https://web.archive.org/web/20060821183345/http://planktonnet.awi.de/ |date=21 August 2006 }}, [[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]]
* [https://web.archive.org/web/20070209042756/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] {{Webarchive|url=https://web.archive.org/web/20160202141717/http://www.ucl.ac.uk/GeolSci/micropal/diatom.html |date=2 February 2016 }}, 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] {{Webarchive|url=https://web.archive.org/web/20091008014752/http://www.rbge.org.uk/science/cryptogamic-plants-and-fungi/phycology/diatoms |date=8 October 2009 }}, [[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]
* [https://web.archive.org/web/20080523203035/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] {{Webarchive|url=https://web.archive.org/web/20110814150634/http://diatom.ansp.org/algae_image/ |date=14 August 2011 }} [[Academy of Natural Sciences of Philadelphia]] (ANSP)
* [http://diatom.ansp.org/nawqa/Taxalist.aspx Diatom taxa] {{Webarchive|url=https://web.archive.org/web/20111003144909/http://diatom.ansp.org/nawqa/Taxalist.aspx |date=3 October 2011 }} [[Academy of Natural Sciences of Philadelphia]] (ANSP)
* [http://www.microscopy-uk.org.uk/diatomist/rbm_US_Royal.pdf An Introduction to the Microscopical Study of Diatoms] {{Webarchive|url=https://web.archive.org/web/20220805070607/http://www.microscopy-uk.org.uk/diatomist/rbm_US_Royal.pdf |date=5 August 2022 }} by Robert B. McLaughlin

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[[Category:Algae]]
[[Category:Diatoms|*]]
<!-- [[Category:Biological oceanography]] [[Category:Planktology]] category:Diatoms already listed -->