Diatoms (Greek: διά (dia) = "through" + τέμνειν (temnein) = "to cut", i.e.

, "cut in half") are a major group of eukaryotic algae, and are

one of the most common types of phytoplankton. Most diatoms are unicellular, although some form chains or simple colonies. A
characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica (hydrated silicon dioxide) called a
frustule. These frustules show a wide diversity in form, some quite beautiful and ornate, but usually consist of two asymmetrical sides
with a split between them, hence the group name. Fossil evidence suggests that they originated during, or before, the early Jurassic
Period.

Domain: Eukaryota
Kingdom: Chromalveolata
Phylum: Heterokontophyta
Class: Bacillariophyceae
Orders
• Centrales

• Pennales

An assortment of Diatomea from Ernst

Haeckel's 1904 Kunstformen der Natur (Artforms of Nature)
There are more than 200 genera of living diatoms, and it is estimated that there are approximately 100,000 extant species[1][2]. Diatoms
are a widespread group and can be found in the oceans, in freshwater, in soils and on damp surfaces. Most live pelagically in open
water, although some live as surface films at the water-sediment interface (benthic), or even under damp atmospheric conditions. They
are especially important in oceans, where they are estimated to contribute up to 45% of the total oceanic primary production[3].
Although usually microscopic, some species of diatoms can reach up to 2 millimetres in length.

Diatoms belong to a large group called the heterokonts, including both autotrophs (e.g. golden algae, kelp) and heterotrophs (e.g.
water moulds). Their yellowish-brown chloroplasts are typical of heterokonts, with four membranes and containing pigments such as
fucoxanthin. Individuals usually lack flagella, but they are present in gametes and have the usual heterokont structure, except they lack
the hairs (mastigonemes) characteristic in other groups.

Most diatom species are non-motile but some are capable of an oozing motion. As their relatively dense cell walls cause them to
readily sink, planktonic forms in open water usually rely on turbulent mixing of the upper layers by the wind to keep them suspended
in sunlit surface waters. Some species actively regulate their buoyancy with intracellular lipids to counter sinking

Diatoms cells are contained within a unique silicate (silicic acid) cell wall comprised of two separate valves (or shells). The biogenic
silica that the cell wall is composed of is synthesised intracellularly by the polymerisation of silicic acid monomers. This material is
then extruded to the cell exterior and added to the wall. Diatom cell walls are also called frustules or tests, and their two valves
typically overlap one other like the two halves of a petri dish. In most species, when a diatom divides to produce two daughter cells,
each cell keeps one of the two valves and grows a smaller valve 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 vegetatively, they
reverse this decline by forming an auxospore. This expands in size to give rise to a much larger cell, which then returns to size-
diminishing divisions. Auxospore production is almost always linked to meiosis and sexual reproduction.

Decomposition and decay of diatoms leads to organic and inorganic (in the form of silicates) sediment, the inorganic component of
which can lead to a method of analyzing past marine environments by corings of ocean floors or bay muds, since the inorganic matter
is embedded in deposition of clays and silts and forms a permanent geological record of such marine strata.

Classification

The classification of heterokonts is still unsettled, and they may be treated as a division (or phylum), kingdom, or something in-
between. Accordingly, groups like the diatoms may be ranked anywhere from class (usually called Bacillariophyceae) to division
(usually called Bacillariophyta), with corresponding changes in the ranks of their subgroups. The diatoms are also sometimes referred
to as Class Diatomophyceae.

Diatoms are traditionally divided into two orders: centric diatoms (Centrales), which are radially symmetric, and pennate diatoms
(Pennales), which are bilaterally symmetric. The former are paraphyletic to the latter. A more recent classification[1] divides the
diatoms into three classes: centric diatoms (Coscinodiscophyceae), pennate diatoms without a raphe (Fragilariophyceae), and pennate
diatoms with a raphe (Bacillariophyceae). It is probable there will be further revisions as understanding of their relationships
increases.

Round & Crawford (1990)[1] and Hoek et al. (1995)[4] provide more comprehensive coverage of diatom taxonomy.

Ecology

A budget of the ocean's silicon cycle[5]

Planktonic forms in freshwater and marine environments typically exhibit a "boom and bust" (or "bloom and bust") lifestyle. When
conditions in the upper mixed layer (nutrients and light) are favourable (e.g. at the start of spring) their competitive edge[6] allows them
to quickly dominate phytoplankton communities ("boom" or "bloom"). As such they are often classed as opportunistic r-strategists
(i.e. those organisms whose ecology is defined by a high growth rate, r).

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
inimical 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[7]), this cycle of bloom, bust, then return to pre-bloom conditions
typically occurs over an annual cycle, with diatoms only being prevalent during the spring and early summer. In some locations,
however, an autumn bloom may occur, caused by the breakdown of summer stratification and the entrainment of nutrients while light
levels are still sufficient for growth. Since vertical mixing is increasing, and light levels are falling as winter approaches, these blooms
are smaller and shorter-lived than their spring equivalents.

In the open ocean, the condition that typically causes diatom (spring) blooms to end is a lack of silicon. Unlike other nutrients, this is
only a major requirement of diatoms so it is not regenerated in the plankton ecosystem as efficiently as, for instance, nitrogen or
phosphorus nutrients. This can be seen in maps of surface nutrient concentrations - as nutrients decline along gradients, silicon is
usually the first to be exhausted (followed normally by nitrogen then phosphorus).

Because of this bloom-and-bust lifestyle, diatoms are believed to play a disproportionately important role in the export of carbon from
oceanic surface waters[8][7] (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[5][9].
Egge & Aksnes (1992)[10] figure
The use of silicon by diatoms is believed by many researchers to be the key to their ecological success. In a now classic study, Egge &
Aksnes (1992)[10] found that diatom dominance of mesocosm communities was directly related to the availability of silicate. When
silicon content approaches a concentration of 2 mmol m-3, diatoms typically represent more than 70% of the phytoplankton
community. Raven (1983)[11] noted that, relative to organic cell walls, silica frustules require less energy to synthesize (approximately
8%), potentially a significant saving on the overall cell energy budget. Other researchers[12] have suggested that the biogenic silica in
diatom cell walls acts as an effective pH buffering agent, facilitating the conversion of bicarbonate to dissolved CO2 (which is more
readily assimilated). Notwithstanding the possible advantages conferred by silicon, diatoms typically have higher growth rates than
other algae of a corresponding size[6].

Evolutionary history

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

The earliest known fossil diatoms date from the early Jurassic (~185 Ma)[13], although recent molecular clock[13] and sedimentary[14]
evidence suggests an earlier origin. It has been suggested that their origin may be related to the end-Permian mass extinction (~250
Ma), after which many marine niches were opened[15]. 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[16]. Since the advent of silicification, diatoms have
made a significant impression on the fossil record, with major deposits of fossil diatoms found as far back as the early Cretaceous, and
some rocks (diatomaceous earth, diatomite, kieselguhr) being composed almost entirely of them.

Although the diatoms may have existed since the Triassic, the timing of their ascendancy and "take-over" of the silicon cycle is more
recent. Prior to the Phanerozoic (before 544 Ma), it is believed that microbial or inorganic processes weakly regulated the ocean's
silicon cycle[17][18][19]. Subsequently, the cycle appears dominated (and more strongly regulated) by the radiolarians and siliceous
sponges, the former as zooplankton, the latter as sedentary filter feeders primarily on the continental shelves[20]. Within the last 100
My, it is thought that the silicon cycle has come under even tighter control, and that this derives from the ecological ascendancy of the
diatoms.

However, the precise timing of the "take-over" is unclear, and different authors have conflicting interpretations of the fossil record.
Some evidence, such as the eviction of siliceous sponges from the shelves[21], suggests that this takeover began in the Cretaceous (146
Ma to 65 Ma), while evidence from radiolarians suggests "take-over" did not begin until the Cenozoic (65 Ma to present)[22].
Nevertheless, regardless of the details of the "take-over" timing, it is clear that this most recent revolution has installed much tighter
biological control over the biogeochemical cycle of silicon.

Collection

Living diatoms are often found clinging in great numbers to filamentous algae, or forming gelatinous masses on various submerged
plants. Cladophora is frequently covered with Cocconeis, an elliptically shaped diatom; Vaucheria is often covered with small forms.
Diatoms frequently present as a brown, slippery coating on submerged stones and sticks, and may be seen to "stream" with river
current.

The surface mud of a pond, ditch, or lagoon will almost always yield some diatoms. They can be made to emerge by filling a jar with
water and mud, wrapping it in black black paper and letting direct sunlight fall on the surface of the water. Within a day, the diatoms
will come to the top in a scum and can be isolated.
Since diatoms form an important part of the food of molluscs, tunicates, and fishes, the alimentary tracts of these animals often yield
forms that are not easily secured in other ways. Marine diatoms can be collected by direct water sampling, though benthic forms can
be secured by scraping barnacles, oyster shells, and other shells.

The silicious shells of diatoms are among the most beautiful objects which can be examined with the microscope. To obtain perfectly
clean mounts requires considerable time and patience, but once the material is cleaned, preparations may be made at any time with
very little trouble.

This section uses text from Methods in Plant Histology.[23]

Genome sequencing

The entire genome of the centric diatom, Thalassiosira pseudonana, has been sequenced[24], and the sequencing of a second diatom
genome from the pennate diatom Phaeodactylum tricornutum is in progress. The first insights into the genome properties of the P.
tricornutum gene repertoire was described using 1,000 ESTs[25]. Subsequently, the number of ESTs was extended to 12,000 and the
Diatom EST Database was constructed for functional analyses[26]. These sequences have been used to make a comparative analysis
between P. tricornutum and the putative complete proteomes from the green alga Chlamydomonas reinhardtii, the red alga
Cyanidioschyzon merolae, and the centric diatom T. pseudonana.[27]

References

1. ^ a b c Round, F. E. and Crawford, R. M. (1990). The Diatoms. Biology and

Morphology of the Genera, Cambridge University Press, UK.

2. ^ Canter-Lund, H. and Lund, J.W.G. (1995). Freshwater Algae, Biopress

Limited. ISBN 0 948737 25 5.

3. ^ Mann, D. G. (1999). The species concept in diatoms. Phycologia 38, 437-

495.

4. ^ Hoek, C. van den, Mann, D. G. and Jahns, H. M. (1995). Algae : An

introduction to phycology, Cambridge University Press, UK.

5. ^ a b Treguer, P., Nelson, D. M., Van Bennekom, A. J., DeMaster, D. J.,

Leynaert, A. and Queguiner, B. (1995). The silica balance in the world
ocean : A reestimate. Science 268, 375-379.

6. ^ a b Furnas, M. J. (1990). In situ growth rates of marine phytoplankton :

Approaches to measurement, community and species growth rates. J.
Plankton Res. 12, 1117-1151.

7. ^ a b Dugdale, R. C. and Wilkerson, F. P. (1998). Silicate regulation of new

production in the equatorial Pacific upwelling. Nature 391, 270-273.
8. ^ Smetacek, V. S. (1985). Role of sinking in diatom life-history cycles :
Ecological, evolutionary and geological significance. Mar. Biol. 84, 239-251.

9. ^ Yool, A. and Tyrrell, T. (2003). Role of diatoms in regulating the ocean's

silicon cycle. Global Biogeochemical Cycles 17, 1103,
doi:10.1029/2002GB002018.

10. ^ a b
Egge, J. K. and Aksnes, D. L. (1992). Silicate as regulating nutrient in
phytoplankton competition. Mar. Ecol. Prog. Ser. 83, 281-289.

11. ^ Raven, J. A. (1983). The transport and function of silicon in plants. Biol.
Rev. 58, 179-207.

12. ^ Milligan, A. J. and Morel, F. M. M. (2002). A proton buffering role for

silica in diatoms. Science 297, 1848-1850.

13. ^ a b
Kooistra, W. H. C. F. and Medlin, L. K. (1996). Evolution of the diatoms
(Bacillariophyta) : IV. A reconstruction of their age from small subunit rRNA
coding regions and the fossil record. Mol. Phylogenet. Evol. 6, 391-407.

14. ^ Schieber, J., Krinsley, D. and Riciputi, L. (2000). Diagenetic origin of

quartz silt in mudstones and implications for silica cycling. Nature 406, 981-
985.

15. ^ Medlin, L. K., Kooistra, W. H. C. F., Gersonde, R., Sims, P. A. and

Wellbrock, U. (1997). Is the origin of the diatoms related to the end-Permian
mass extinction? Nova Hedwegia 65, 1-11.

16. ^ Raven, J. A. and Waite, A. M. (2004). The evolution of silicification in

diatoms : inescapable sinking and sinking as escape? New Phytologist 162,
45-61.

17. ^ Siever, R. (1991). Silica in the oceans : biological-geological interplay. In :

Schneider, S. H., Boston, P. H. (eds.), Scientists On Gaia, The MIT Press,
Cambridge MA, USA, pp. 287-295.
 18. ^ Kidder, D. L. and Erwin, D. H. (2001). Secular distribution of biogenic
silica through the Phanerozoic : Comparison of silica-replaced fossils and
bedded cherts at the series level. J. Geol. 109, 509-522.

19. ^ Grenne, T. and Slack, J. F. (2003). Paleozoic and Mesozoic silic-rich

seawater : evidence from hematitic chert (jasper) deposits. Geology 31, 319-
322.

20. ^ Racki, G. and Cordey, F. (2000). Radiolarian palaeoecology and

radiolarites : is the present the key to the past? Earth-Science Reviews 52, 83-
120.

21. ^ Maldonado, M., Carmona, M. C., Uriz, J. M. and Cruzado, A. (1999).

Decline in Mesozoic reef-building sponges explained by silicate limitation.
Nature 401, 785-788.

22. ^ Harper, H. E. and Knoll, A. H. (1975). Silica, diatoms, and Cenozoic

radiolarian evolution. Geology 3, 175-177.

23. ^ Chamberlain, C. J. (1901) Methods in Plant Histology, University of

Chicago Press, USA

24. ^ Armbrust et al. (2004). The genome of the diatom Thalassiosira

pseudonana: ecology, evolution, and metabolism. Science 306, 79-86.

Diatoms: Biology, Ecology, Taxonomy, Morphology

What are diatoms? One celled plants belonging into the plant class Bacilariophyceae of the division or phylum Bacilariophyta.
Diatoms are either solitary and free, attached to a substratum by gelatinous extrusions or joined to each other in chains of varying
length. Some species are capable of active movement but others are merely free floating and depend on currents for transport.
Individual diatoms range in size from 2 microns to several millimeters, although there only very species that are larger than 200
microns. The actual number of extinct and extant diatom species may well be over 50.000.

Where do they occur? Diatoms are distributed throughout the world in aquatic, semi-aquatic and moist habitats. They are found in
the sea, estuaries, freshwater lakes, ponds, streams, and ditches. More rigorous habitats such as moist rocks or soils or damp bark
sometimes support lush growths of diatoms.
Though individual diatom cells are microscopic, masses of diatoms can often be seen on stream bottoms, along the surf zones, during
plankton blooms as brownish colored waters or films.
See the left panel for some illustrations of different habitat
BACILLARIOPHYTA

Diatoms are unicells that share the feature of having a cell wall made of silicon dioxide. This opaline or
glass frustule is composed of two parts (valves), which fit together with the help of a cingulum or set of
girdle bands.

The taxonomy of diatoms is based in large part on the shape and structure of the siliceous valves.
Although some species can be identified in the living state, and some genera were and have been erected
based on the organization and fate of cytoplasmic organelles, species-level identification usually requires
examination with oil immersion objectives of permanently-mounted specimens. To accomplish this,
diatoms are "cleaned" to rid them of their organic components. Cleaning is done by oxidizing diatom
material in potassium dichromate (van der Wurff 1954). After washing the cleaned material (which will
appear white) several times in distilled water, it is dried onto a coverslip which is then mounted onto a
glass slide with Hyrax or other mounting medium with a high refractive index (Naphrax).

Two major groups of diatoms are generally recognized: the centric diatoms exhibit radial symmetry
(symmetry about a point) and have oogamous sexual reproduction, while the pennate diatoms are
bilaterally symmetrical (symmetry about a line) and produce ameboid gametes that are morphologically
similar but may be physiologically different. Chloroplasts of diatoms are variable, but consistent within
most taxa. Chloroplasts may be many small discs, a condition found in most centric diatoms and some
(araphid) pennates, or few large, plate-like chloroplasts are found in the majority of pennate taxa.

Diatoms live in most freshwater systems, including a wide range of pH, organic pollution, and
temperatures. Cells occur singly or in colonies, some of which are visible to the naked eye. Mucilage is
secreted by most diatoms and it covers the exterior of the frustule. Mucilage is also used to produce a
diversity of growth forms/habits. Diatoms may grow at the ends of mucilaginous stalks (e.g. Achnanthes,
Gomphonema) or within mucilaginous tubes (e.g. Encyonema). Mucilage is also employed to hold parts of
different cells together in chains (e.g. Tabellaria, Diatoma) or in stellate colonies (Asterionella). Colony
formation is also accomplished in diatoms by interdigitation of siliceous spines on the valve margins of
adjoining cells (e.g. Fragilaria, Aulacoseira).

Through the life cycle of these diploid organisms (see Kociolek and Williams 1988 for a review) cell size
decreases, as each valve of a frustule produces a smaller, complementary valve. Accompanying size
diminution are changes in outline and, but less frequently, ornamentation (see Stoermer and Ladewski
1982; Stoermer et al. 1986 for examples). After sexual reproduction, which is accomplished through
meiosis, the small zygote enlarges to form an auxospore, a mostly non-siliceous stage that has siliceous
strips or scales covering it. The stage next produces a valve. The initial valve represents that largest valve
in the cell cycle. Hence, sex accomplishes genetic variability and allow a cell line to regain maximum size
before the next round of vegetative (mitotic) cell divisions. Diminution accompanies vegetative cell
division until a certain size range is reached where, when environmental parameters are also right, sexual
reproduction is induced. Most diatomists have considered the diminution of diatoms through their
ontogeny a consequence of having rigid cell walls, but Lewis (1984) interprets the diminution cycle as a
timing mechanism or adaptation ("sex clock") for sex in these unicells.

Although diatomists speak of vegetative cell division resulting in high degree of fidelity in diatom
morphology, variability occurs within and between cell lines in a population and between populations. This
has important implications for the identification of diatoms at the species and subspecific levels. The effect
of cell division and the distribution of resulting sizes (e.g. ), variability in size, shape and ornamentation
may occur within and between descendants of one or more individuals. Diatom taxonomists usually
distinguish taxa based on a lack of intermediates between ranges of variability (see Theriot and Stoermer
1984; Kociolek and Stoermer 1991 for examples of this approach). However, heterovalvy may occur within
individuals so that valves of a frustule possess the ornamentation of different "taxa" although no
intermediate morphologies occur (e.g. Stoermer 1967). Obviously, in this case, the two "taxa" must be
considered as one. In addition, differences in environmental conditions (e.g. salt concentrations, silica
levels; e.g. Tuchman et al. 1984) can alter morphology within a taxon. All of these factors must be
considered when attempting species-level identifications.

Critical examination of diatoms valves with light and electron microscopy has led to a proliferation of
terms associated with the minutiae of valve morphology. Given the excellent, recent treatments of Round
et al. (1990) and Krammer and Lange-Bertalot (1986, 1988, 1991) with regard to diatom ultrastructure, it
seems redundant to provide a detailed treatment here. Terminology necessary to work through the keys
and descriptions of genera is presented in the glossary.
Two taxonomic works have been mainstays in the libraries of diatomists in this country. Patrick and
Reimer's (1966, 1975) excellent tomes, The Diatoms of the United States , which does not include centrics
or most of the problematic keel-bearing taxa (e.g. Nitzschia) have been complemented by the classic work
by Hustedt (1930). This latter work has been updated in a 4 volume set by Krammer and Lange-Bertalot
(1986, 1988, 1991). Other works of utility to freshwater ecologists in identifying diatoms include Cleve-
Euler (1951-1955), Hustedt (1927-1966), Simonsen (1989), Van Heurk (1880-1885) and Schmidt et al.
(1854-1959).

The present work deviates somewhat from past taxonomic treatments of diatoms, particularly those
included in large treatises of freshwater algae in North America (e.g. Smith 1950; Prescott 1951). These
treatises relied heavily on other, older treatments of diatoms (e.g. Boyer 1927 in Smith's work) or gave
diatoms only peripheral consideration (e.g. Prescott's work). The work presented herein represents our
own treatment of the flora in the region, based on our own collections. In addition, the taxonomy of
diatoms has undergone a revolution in the last 15 years, with many new taxa (particularly at the genus
level) being proposed on ultrastructural characteristics. Many of these (e.g. Aulacoseira) have gained
acceptance by diatom taxonomists, but have not found their way into general usage in the phycological
literature. The work by Round et al. (1990), for all of its shortcomings (e.g. Kociolek 1991), has led to the
recognition of many new taxa, several of which are followed in the present work (e.g. Luticola and
Sellaphora, taxa considered part of Navicula in more classical treatments). We make reference to the older
names and literature in the generic descriptions, so that ecological or distributional data may be gleaned
for these taxa from the older literature. Other taxonomic proposals (the splitting or lumping of the araphid
genera Fragilaria and Synedra; Williams and Round 1988, 1989; Lange-Bertalot 1991), which have serious
implications for the way we deal with diatom taxonomy, have not been followed here, pending further
arguments and evidence from both sides.

Diatoms are single-celled organisms which secrete intricate skeletons. These may be elongate, with a bilateral plane of symmetry, or
they may be round and radially symmetrical. Many diatoms are slightly asymmetrical, though they generally fall into one of these two
categories.

The skeleton of a diatom, or frustule, is made of very pure silica coated with a layer of organic material. This skeleton is divided into
two parts, one of which (the epitheca) overlaps the other (the hypotheca) like the lid of a box or petri dish. Observe the diatom
frustule below at right, in which the two halves have been pushed slightly askew. Both epitheca and hypotheca are made up of two or
more parts: the valve, a more or less flattened plate, and at least one cingulum, a hoop-like rim. This electron micrograph (below at
left) shows the inside of a single valve of Cocconeis.

As is visible in the photographs, both parts of a frustule may be highly perforated. Pennate diatoms show a long slit, the raphe, along
the long axis. Through the raphe, the living diatom secretes mucilage, with which it may attach to a substrate or move by gliding over
the substrate.

Within their silica walls, diatoms show a typical level of eukaryote organization. Living diatoms contain several chloroplasts, where
photosynthesis takes place.