Diatom

Diatoms (Greek:  (dia) = "through" +  (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.

General biology


There are more than 200 genera of living diatoms, and it is estimated that there are approximately 100,000 extant species. 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. 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 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) and Hoek et al. (1995) provide more comprehensive coverage of diatom taxonomy.

Ecology


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 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 ), 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 (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.



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) 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) 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 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.

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), although recent molecular clock and sedimentary evidence suggests an earlier origin. It has been suggested that their origin may be related to the end-Permian mass extinction (~250 Ma), after which many marine niches were opened. The gap between this event and the time that fossil diatoms first appear may indicate a period when diatoms were unsilicified and their evolution was cryptic. 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. 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. 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, 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). 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 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.

Genome sequencing
The entire genome of the centric diatom, Thalassiosira pseudonana, has been sequenced, 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. Subsequently, the number of ESTs was extended to 12,000 and the Diatom EST Database was constructed for functional analyses. These sequences have been used to make a comparative analysis between P. tricornutum and the putative complete proteomes from the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana.