Amoeba
Terminology
There are many closely related terms that can be the source of confusion:

Amoeba is a genus that includes species such as Amoeba proteus

Amoebidae is a family that includes the Amoeba genus, among others.

Protista is a kingdom that includes the Amoebidae family, among others.

Amoeboids are organisms that move by crawling. Many (but not all) amoeboids are Amoebozoa.
History
The amoeba was first discovered by August Johann Rösel von Rosenhof in 1757.[2] Early naturalists referred to Amoeba as
the Proteus animalcule after the Greek god Proteus who could change his shape. The name "amibe" was given to it by Bory de SaintVincent,[3] from the Greek amoibè (αμοιβή), meaning change.[4]Dientamoeba fragili was first described in 1918, and was linked to
harm in humans.[5]
Anatomy
Anatomy of an amoeba
The cell's organelles and cytoplasm are enclosed by a cell membrane, obtaining its food through phagocytosis. Amoebae have a
single large tubular pseudopod at the anterior end, and several secondary ones branching to the sides. The most famous
species, Amoeba proteus, averages about 220-740 μm in length while moving,[6] making it a giant among amoeboids.[7] A few
amoeboids belonging to different genera can grow larger, however, such as Gromia, Pelomyxa, and Chaos.
Amoebae's most recognizable features include one or more nuclei and a simple contractile vacuole to maintain osmotic equilibrium.
Food enveloped by the amoeba is stored and digested in vacuoles. Amoebae, like other single-celled eukaryotic organisms,
reproduce asexually via mitosis and cytokinesis, not to be confused with binary fission, which is how prokaryotes (bacteria)
reproduce. In cases where the amoeba are forcibly divided, the portion that retains the nucleus will survive and form a new cell and
cytoplasm, while the other portion dies. Amoebae also have no definite shape. [8]
Genome
The amoeba is remarkable for its very large genome. The species Amoeba proteus has 290 billion (10^9) base pairs in its genome,
while the related Polychaos dubium (formerly known as Amoeba dubia) has 670 billion base pairs. The human genome is small by
contrast, with its count of 2.9 billion bases.[9]
Osmoregulation
Like most other protists, amoebas have a contractile vacuole complex. Amoeba proteus, a free-living, freshwater species of amoeba,
has one contractile vacuole (CV) which is amembrane-bound organelle. The CV slowly fills with water from the cytoplasm (diastole)
and whilst fusing with the cell membrane, it quickly contracts releasing water to the outside (systole) by exocytosis. This process
regulates the amount of water present in the cytoplasm of the amoeba; it is therefore a means of osmoregulation.
Immediately after the CV expels water, its membrane crumples, and soon afterwards, many small vacuoles or vesicles appear
surrounding the membrane of the CV.[10] It is suggested that these vesicles split from the CV membrane itself. The small vesicles
gradually increase in size as they take in water and then they fuse with the CV, which grows in size as it fills with water. Therefore,
the function of these numerous small vesicles is to collect excess cytoplasmic water and channel it to the central CV. The CV swells
for a number of minutes and then contracts to expel the water outside. The cycle is then repeated again.
The membranes of the small vesicles as well as the membrane of the CV have aquaporin proteins embedded in
them.[10] These transmembrane proteins facilitate water passage through the membranes. The presence of aquaporin proteins in
both CV and the small vesicles suggests that water collection occurs both through the CV membrane itself as well as through the
function of the vesicles. However, the vesicles, being more numerous and smaller, would allow a faster water uptake due to the
larger total surface area provided by the vesicles.[10]
The small vesicles also have another protein embedded in its membrane; Vacuolar-type H+-ATPase or V-ATPase.[10] This ATPase
pumps H+ ions into the vesicle lumen, lowering its pH with respect to the cytosol. However, the pH of the CV in some amoebas is
only mildly acidic, suggesting that the H+ ions are being removed from the CV or from the vesicles. It is thought that the
electrochemical gradient generated by V-ATPase might be used for the transport of ions (probably K+ and Cl-) into the vesicles. This
builds an osmotic gradient across the vesicle membrane, leading to influx of water from the cytosol into the vesicles by
osmosis,[10] which is facilitated by aquaporins.
Since these vesicles fuse with the central contractile vacuole which expels the water out, ions end up being removed from the cell,
which is not beneficial for a freshwater organism. The removal of ions with the water has to be compensated by some as yet
unidentified mechanism.
Like most cells, amoebae are adversely affected by excessive osmotic pressure caused by extremely saline or dilute water. Amoebae
will prevent the influx of salt in saline water, resulting in a net loss of water as the cell becomes isotonic with the environment,
causing the cell to shrink. Placed into fresh water, amoebae will also attempt to match the concentration of the surrounding water,
causing the cell to swell and sometimes burst if the water surrounding the amoeba is too dilute.[11]
Amoebic cysts
In environments which are potentially lethal to the cell, an amoeba may become dormant by forming itself into a ball and secreting a
protective membrane to become a microbial cyst. The cell remains in this state until it encounters more favourable
conditions.[8] While in cyst form the amoeba will not replicate and may die if unable to emerge for a lengthy period of time.
Marine amoeba
Marine amoeba lack contractile vacuoles and their enzymes and organelles are not damaged by the salt water found in seas, oceans,
salt swamps, salty rivers and ponds. Most are microscopic, but some can grow as large as grapes. [12]
Euglena
Euglena is a genus of unicellular protists, of the class Euglenoidea of the phylum Euglenozoa (also known as Euglenophyta). They are
single-celled organisms. Currently, over 1,000 species of Euglena have been described. There are many to be discovered. Marin et
al.(2003) revised the genus to include several species without chloroplasts, formerly classified as Astasia and Khawkinea. Some
Euglena are considered to have both plant and animal features. Due to these dual characteristics, much debate has arisen to how
they have evolved, and into which clade they should be placed. In binomial nomenclature, according to the five-kingdom
classification scheme, euglena have been accurately placed into Kingdom Protista, more specifically into Subkingdom Protozoa, and
even more specifically into Phylum Mastigophora, which use flagellum as a method of locomotion.
Form and function
A diagram ofEuglena
Euglena is a protist that can both eat food as animals by heterotrophy; and can photosynthesize, like plants, by autotrophy. When
acting as a heterotroph, the Euglena surrounds a particle of food and consumes it by phagocytosis. When acting as an autotroph, the
Euglena utilizes chloroplasts, (hence green color) containing Chlorophyll a, Chlorophyll b, and some carotenoid pigments, to produce
sugars by photosynthesis. Each chloroplast has three membranes, and exist in thylakoid stacks of three. The number and shape of
chloroplasts within euglenozoa varies greatly due to environmental conditions and evolutionary history. Euglena are able to move
through aquatic environments by using a large flagellum for locomotion. To observe its environment, the cell contains aneyespot, a
primitive organelle that filters sunlight into the light-detecting, photo-sensitive structures at the base of the flagellum; allowing only
certain wavelengths of light to hit it. This photo-sensitive area detects the light that is able to be transmitted through the eyespot.
When such light is detected, the Euglena may accordingly adjust its position to enhance photosynthesis. The mobility of Euglena also
allows for hunting capability, because of this adaptation, many Euglena are considered mixotrophs: autotrophs in sunlight
and heterotrophs in the dark. Euglena also structurally lack cell walls, but have a pellicleinstead. The pellicle is made of protein
bands that spiral down the length of the Euglena and lie beneath the plasma membrane.
Euglena can survive in fresh and salt water. In low moisture conditions, a Euglena forms a protective wall around itself and lies
dormant as a spore until environmental conditions improve. Euglena can also survive in the dark by storing paramylon granules in
pyernoid bodies within the chloroplast.
Reproduction
Euglenas reproduce asexually, and there has been no evidence of sexual reproduction. Reproduction includes transverse division
and longitudinal division, which both occur in the active and encysted forms. Acidity and alkalinity have been known to affect
reproduction and life spans of Euglenozoans. Life spans also greatly differ between each group of Euglenozoans.
Gallery
Foraminifera
Foraminifera
Temporal range: Precambrian Recent
Live Ammonia tepida (Rotaliida)
Scientific classification
Domain:
Eukaryota
Kingdom:
Rhizaria
Superphylum:
Retaria
Phylum:
Foraminifera
d'Orbigny, 1826
The Foraminifera, ("hole bearers") or forams for short, are a large group of amoeboid protists with reticulating pseudopods, fine
strands ofcytoplasm that branch and merge to form a dynamic net.[1] They typically produce a test, or shell, which can have either
one or multiple chambers, some becoming quite elaborate in structure.[2] These shells are made of calcium carbonate (CaCO 3) or
agglutinated sediment particles. About 275,000 species are recognized, both living and fossil. They are usually less than 1 mm in size,
but some are much larger, and the largest recorded specimen reached 19 cm.
Taxonomic relations
Foraminifera are typically included in the Kingdom Protozoa, [3][4][5] although some taxonomies put them in the
equivalent Protoctista[6] or Protista.[7] There is also compelling evidence, based primarily on molecular evidence, for their belonging
to a major group within the Protozoa known as the Rhizaria.[3] Prior to the recognition of the Rhizaria as a taxon, Foraminifera were
generally place in the Class Granuloreticulosa, Phylum Rhizopodea (or Sarcodina). This morphology based perspective remains in use
today.
Rhizaria is somewhat problematical as it is often referred to simply as a "supergroup", which may account for its sometimes overelevated status, although Cavalier-Smith does define it as an infrakingdom within the Kingdom Protozoa. [3] Otherwise Rhizaria could
easily be recognized as a phylum, equivalent to the Rhizopodea which it replaces.
The taxonomic position of Foraminifera has varied since their recognition as protozoa (protists) by Schultze in 1854, [8] most often
being referred to as an order, but sometimes a class. Leoblich and Tappan (1992) [9] redefined Foraminifera as a class from its
previous ordinal rank (as Foraminiferida) in the Treatise, where it now sits. Some taxonomies go so far as to put foraminifera in
phylum of their own, putting them on par with the amoeboid Sarcodina in which they had been placed.
Although as yet unsupported by morphological correlates, molecular data strongly suggest that Foraminifera are closely related to
theCercozoa and Radiolaria, both of which also include amoeboids with complex shells; these three groups make up
the Rhizaria.[4] However, the exact relationships of the forams to the other groups and to one another are still not entirely clear.
[edit]Living forams
Modern forams are primarily marine, although some can survive in brackish conditions. [10] They are most commonly benthic, and
about 40 morphospecies are planktonic.[1] This count may however represent only a fraction of actual diversity, since many
genetically discrepant species may be morphologically indistinguishable. [11]
A number of forms have unicellular algae as endosymbionts, from diverse lineages such as the green algae, red algae, golden
algae, diatoms, and dinoflagellates.[1] Some forams arekleptoplastic, retaining chloroplasts from ingested algae to
conduct photosynthesis.[12]
Biology
The foraminiferal cell is divided into granular endoplasm and transparent ectoplasm from which a pseudopodial net may emerge
through a single opening or through many perforations in the test. Individual pseudopods characteristically have small granules
streaming in both directions.[10] The pseudopods are used for locomotion, anchoring, and in capturing food, which consists of small
organisms such as diatoms or bacteria.[1]
The foraminiferal life-cycle involves an alternation between haploid and diploid generations, although they are mostly similar in
form.[8][13] The haploid or gamont initially has a singlenucleus, and divides to produce numerous gametes, which typically have
two flagella. The diploid or schizont is multinucleate, and after meiosis fragments to produce new gamonts. Multiple rounds
of asexual reproduction between sexual generations is not uncommon in benthic forms.[10]
Tests
Thin section of a peneroplid foraminiferan from Holocene lagoonal sediment in Rice Bay, San Salvador Island, Bahamas. Scale bar
100 micrometres.
The form and composition of the test is the primary means by which forams are identified and classified. Most have calcareous tests,
composed of calcium carbonate.[10] In other forams the test may be composed of organic material, made from small pieces of
sediment cemented together (agglutinated), and in one genus of silica. Openings in the test, including those that allow cytoplasm to
flow between chambers, are called apertures.
Tests are known as fossils as far back as the Cambrian period,[14] and many marine sediments are composed primarily of them. For
instance, the limestone that makes up the pyramids of Egypt is composed almost entirely of nummulitic benthic
foraminifera.[15] Production estimates indicate that reef foraminifera annually generate approximately 43 million tons of calcium
carbonate and thus play an essential role in the production of reef carbonates. [16]
Genetic studies have identified the naked amoeba "Reticulomyxa" and the peculiar xenophyophores as foraminiferans without tests.
A few other amoeboids produce reticulose pseudopods, and were formerly classified with the forams as the Granuloreticulosa, but
this is no longer considered a natural group, and most are now placed among the Cercozoa. [17]
Deep sea species
Foraminifera are found in the deepest parts of the ocean such as the Mariana Trench, including the Challenger Deep, the deepest
part known. At these depths, below the carbonate compensation depth, the calcium carbonate of the tests is soluble in water due to
the extreme pressure. The foraminifera found in the Challenger Deep thus have no carbonate test, but instead have one of organic
material.[18]
Four species have been found in the Challenger Deep that are unknown from any other place in the ocean, one of which is
representative of an endemic genus unique to the region. They are Resigella laevis and R. bilocularis, Nodellum aculeata,
and Conicotheca nigrans (the unique genus). All have tests that are mainly of transparent organic material which have small (~
100 nm) plates that appears to be clay [18]
Evolutionary significance
Dying planktonic foraminifera continuously rain down on the sea floor in vast numbers, their mineralized tests preserved as fossils in
the accumulating sediment. Beginning in the 1960s, and largely under the auspices of the Deep Sea Drilling, Ocean Drilling, and
International Ocean Drilling Programmes, as well as for the purposes of oil exploration, advanced deep-sea drilling techniques have
been bringing up sediment cores bearing foraminifera fossils by the millions. The effectively unlimited supply of these fossil tests and
the relatively high-precision age-control models available for cores has produced an exceptionally high-quality planktonic
foraminifera fossil record dating back to the mid-Jurassic, and presents an unparalleled record for scientists testing and documenting
the evolutionary process. The exceptional quality of the fossil record has allowed an impressively detailed picture of species interrelationships to be developed on the basis of fossils, in many cases subsequently validated independently through molecular genetic
studies on extant specimens. Larger benthic foraminifera with complex shell structure react in a highly specific manner to the
different benthic environments and, therefore, the composition of the assemblages and the distribution patterns of particular
species reflect simultaneously bottom types and the light gradient. In the course of Earth history, larger foraminifera are replaced
frequently. In particular, associations of foraminifera characterizing particular shallow water facies types are dying out and are
replaced after a certain time interval by new associations with the same structure of shell morphology, emerging from a new
evolutionary process of adaptation. These evolutionary processes make the larger foraminifera prone to be fossil index for the
Permian, Jurassic, Cretaceous and Cenozoic (e.g. Lukas Hottinger).
Uses of forams
Because of their diversity, abundance, and complex morphology, fossil foraminiferal assemblages are useful for biostratigraphy, and
can accurately give relative dates to rocks. The oil industry relies heavily on microfossils such as forams to find potential oil
deposits.[19]
Calcareous fossil foraminifera are formed from elements found in the ancient seas they lived in. Thus they are very useful
in paleoclimatologyand paleoceanography. They can be used to reconstruct past climate by examining the stable isotope ratios of
oxygen, and the history of the carbon cycle and oceanic productivity by examining the stable isotope ratios of
carbon;[20] see δ18O and δ13C. Geographic patterns seen in the fossil records of planktonic forams are also used to reconstruct
ancient ocean currents. Because certain types of foraminifera are found only in certain environments, they can be used to figure out
the kind of environment under which ancient marine sediments were deposited.
For the same reasons they make useful biostratigraphic markers, living foraminiferal assemblages have been used as bioindicators in
coastal environments, including indicators of coral reef health. Because calcium carbonate is susceptible to dissolution in acidic
conditions, foraminifera may be particularly affected by changing climate and ocean acidification.
Foraminifera can also be utilised in archaeology in the provenancing of some stone raw material types. Some stone types, such
as chert, are commonly found to contain fossilised foraminifera. The types and concentrations of these fossils within a sample of
stone can be used to match that sample to a source known to contain the same "fossil signature".
Diatom
Diatoms
Marine diatoms.
Scientific classification
Domain:
Eukaryota
Kingdom:
Chromalveolata
Phylum:
Heterokontophyta
Class:
Bacillariophyceae
Haeckel 1878
Orders

Centrales

Pennales
A diatom. Numbered ticks are 10 microns apart.
Diatoms[1] are a major group of algae, and are one of the most common types of phytoplankton. Most diatoms are unicellular,
although they can exist as colonies in the shape of filaments or ribbons (e.g. Fragillaria), fans (e.g. Meridion), zigzags (e.g. Tabellaria),
or stellate colonies (e.g. Asterionella). Diatoms are producers within the food chain. 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, 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. Diatom communities are a popular tool for monitoring
environmental conditions, past and present, and are commonly used in studies of water quality.
General biology
There are more than 200 genera of living diatoms, and it is estimated that there are approximately
100,000 extant species.[2][3][4] 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.[5] Spatial distribution of marine phytoplankton species is restricted both horizontally and
vertically.[6] Diatoms occur in all oceans from the poles to the tropics; polar and subpolar regions contain relatively few species
compared with temperate biota. Although tropical regions exhibit the greatest number of species, more abundant populations are
found in polar to temperate regions.[7] 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 thecarotenoid 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 diatoms are nonmotile, although some move via flagellation. 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 intracellularlipids to counter sinking.
Diatom cells are contained within a unique silicate (silicic acid) cell wall comprising 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 over the other like the two halves of a petri dish. In most species, when a diatom divides to produce two daughter cells,
each cell keeps one of the two halves and grows a smaller half within it. As a result, after each division cycle the average size of
diatom cells in the population gets smaller. Once such cells reach a certain minimum size, rather than simply divide 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 sizediminishing 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.
The study of diatoms is a branch of phycology, and phycologists specializing in diatoms are called diatomists.
Classification
Selections from Ernst Haeckel's 1904Kunstformen der Natur (Artforms of Nature), showing pennate (left) and centric (right)
frustules.
Diatomaceous earth as viewed under bright fieldillumination on a light microscope. Diatomaceous earth is a
soft, siliceous, sedimentary rock made up of the cell walls ofdiatoms and readily crumbles to a fine powder. This sample consists of a
mixture of centric (radially symmetric) and pennate (bilaterally symmetric) diatoms. This image of diatomaceous earth particles
in water is at a scale of 6.236 pixels/μm, the entire image covers a region of approximately 1.13 by 0.69 mm.
The classification of heterokonts is still unsettled, and they may be treated as a division (or phylum), kingdom, or something inbetween. Accordingly, groups like the diatoms may be ranked anywhere from class (usually called Diatomophyceae) to division
(usually called Bacillariophyta), with corresponding changes in the ranks of their subgroups.
Diatoms are traditionally divided into two orders:

centric diatoms (Centrales), which are radially symmetric

pennate diatoms (Pennales), which are bilaterally symmetric. The former are paraphyletic to the latter.
A more recent classification[3] divides the diatoms into three classes:

centric diatoms (Coscinodiscophyceae)

pennate diatoms

without a raphe (Fragilariophyceae)

with a raphe (Bacillariophyceae)
It is probable there will be further revisions as understanding of their relationships increases. [8]
Diatoms generally range in size from ca. 2-200μm,[2] and are composed of a cell wall comprising silica.[7] This siliceous wall can be
highly patterned with a variety of pores, ribs, minute spines, marginal ridges and elevations; all of which can be utilised 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, typically
though the shape of the cell is circular, although, some cells may be triangular, square, or elliptical.
Cells are solitary or united into colonies of various kinds, which may be linked by siliceous structures; mucilage pads, or stalks;
mucilage tubes; amorphous masses of mucilage and threads of polysaccharide (chitin), which are secreted through strutted
processes. Major pigments of diatoms are chlorophylls a and c, beta-carotene, fucoxanthin, diatoxanthin and
diadinoxanthin.[2]Diatoms are primarily photosynthetic. A few, however, are obligate heterotrophs, while others can live
heterotrophically in the absence of light, provided an appropriate organic carbon source is available. Storage products
are chrysolaminarin and lipids.[7]
Round & Crawford (1990)[3] and Hoek et al. (1995)[9] provide more comprehensive coverage of diatom taxonomy.
Ecology
A budget of the ocean's silicon cycle[10]
Planktonic diatoms in freshwater and marine environments typically exhibit a "boom and bust" (or "bloom and bust") lifestyle.
When conditions in the upper mixed layer (nutrients and light) are favourable (e.g. at the start of spring) their competitive
edge[11]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
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[12]), 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 cycle, diatoms are believed to play a disproportionately important role in the export of carbon from
oceanic surface waters[12][13] (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.[10][14]
Egge & Aksnes (1992)[15] 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)[15] found that diatom dominance of mesocosm communities was directly related to the availability of silicic acid —
when concentrations were greater than 2 mmol m−3, they found that diatoms typically represented more than 70% of the
phytoplankton community. Raven (1983)[16] noted that, relative to organic cell walls, silica frustules require less energy to synthesize
(approximately 8% of a comparable organic wall), potentially a significant saving on the overall cell energy budget. Other
researchers[17] 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. [11]
Diatoms occur in virtually every environment that contains water. This includes not only oceans, seas, lakes and streams, but also
soil.
Life-Cycle
Sexual reproduction of a centric diatom (oogamy)
Sexual reproduction of a pinnate diatom (morphological isogamy, physiological anisogamy)
Diatoms are non-motile; however, sperm found in some species can be flagellated, though motility is usually limited to a gliding
motion.[7]Reproduction among these organisms is primarily asexual by binary fission, with each daughter cell receiving one of the
parent cell's two frustules (or theca). This is used by each daughter cell as the larger frustule (or epitheca) into which a second, small
frustule (or hypotheca) is constructed.
This form of division results in a size reduction of the offspring and therefore the average cell size of a diatom population decreases,
until the cells are about one-third their maximum size.[2] It has been observed, however, the ability of certain taxa to divide without
causing a reduction in cell size.[18] Nonetheless, in order to restore the cell size of a diatom population for those that do endure size
reduction, sexual reproduction andauxospore formation must occur.[2] 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. [7]
In centric diatoms, the small male gametes have one flagellum while the female gametes are large and non-motile (oogamous).
Conversely, in pinnate diatoms both gametes lack flagella (isoogamous).[2] Certain araphid species have been documented as
anisogamous and are, therefore, considered to represent a transitional stage between centric and pinnate diatoms. [18]
Evolutionary history
Heterokont chloroplasts appear to be derived from those of red algae, rather than directly from prokaryotes as occurred 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),[19] although molecular
clock[19] and sedimentary[20] evidence suggests an earlier origin. It has been suggested that their origin may be related to the endPermian mass extinction (~250 Ma), after which many marineniches were opened.[21] 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.[22] 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.[23][24][25]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.[26] Within the last 100
My, it is thought that the silicon cycle has come under even tighter control, and that this derives from the ecological ascendancy of
the diatoms.
However, the precise timing of the "take-over" is unclear, and different authors have conflicting interpretations of the fossil record.
Some evidence, such as the displacement of siliceous sponges from the shelves, [27] suggests that this takeover began in the
Cretaceous (146 Ma to 65 Ma), while evidence from radiolarians suggests "take-over" did not begin until theCenozoic (65 Ma to
present).[28] The expansion of grassland biomes and the evolutionary radiation of grasses during the Miocene is believed to have
increased the flux of soluble silicon to the oceans, and it has been argued that this has promoted the diatoms during the Cenozoic
era.[29][30] However, work on the variation of diatom diversity during the Cenozoic suggests instead that diatom success is decoupled
from the evolution of grasses, and that diatoms were most diverse prior to the diversification of grasses. [31] 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.
[edit]Fossil record
The fossil record of diatoms has largely been established through the recovery of their siliceous frustules 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.[32] Where diatombiozones are well established and calibrated to the geomagnetic polarity time
scale (e.g., Southern Ocean, North Pacific, eastern equatorial Pacific), diatom-based age estimates may be resolved to within
<100,000 years, although typical age resolution for Cenozoic diatom assemblages is several hundred thousand years.
The Cretaceous record of diatoms is limited, but recent studies reveal a progressive diversification of diatom types. The CretaceousTertiary extinction event, which in the oceans dramatically affected organisms with calcareous skeletons, appears to have had
relatively little impact on diatom evolution.[33]
Although no mass extinctions of marine diatoms have been observed during the Cenozoic, times of relatively rapid evolutionary
turnover in marine diatom assemblages occurred near thePaleocene–Eocene boundary[34] and at the Eocene–
Oligocene boundary.[35] Further turnover of assemblages took place at various times between the middle Miocene and
latePliocene,[36] 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.[32] This coincides with an
increasingly more vigorous circulation of the ocean’s surface and deep waters brought about by increasing latitudinal thermal
gradients at the onset of major ice sheet expansion on Antarctica and progressive cooling through
the Neogene and Quaternary towards a bipolar glaciated world. This drove the diatoms into uptaking silica more competitively (i.e.,
to use less silica in formation of their 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.
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 withCocconeis, an elliptically shaped diatom; Vaucheria is often covered with small forms.
Diatoms are frequently present as a brown, slippery coating on submerged stones and sticks, and may be seen to "stream" with river
current.
The surface mud of a pond, ditch, or lagoon will almost always yield some diatoms. They can be made to emerge by filling a jar with
water and mud, wrapping it in black paper and letting direct sunlight fall on the surface of the water. Within a day, the diatoms will
come to the top in a scum and can be isolated.
Since diatoms form an important part of the food of 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.
This section uses text from Methods in Plant Histology.[37]
EST sequencing
The first insights into the properties of the P. tricornutum gene repertoire was described using 1,000 ESTs.[38] Subsequently, the
number of ESTs was extended to 12,000 and the Diatom EST Database was constructed for functional analyses.[39] 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 T. pseudonana.[40] The diatom EST database now
consists in 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 corresponding to different abiotic stresses (available athttp://www.biologie.ens.fr/diatomics/EST3/).[41]
Genome sequencing
The entire genomes of the centric diatom, Thalassiosira pseudonana (32.4 Mb),[42] and the pennate diatom, Phaeodactylum
tricornutum (27.4 Mb),[43] have been sequenced. Comparisons of the two fully sequenced diatom genomes finds that the P.
tricornutum genome includes fewer genes (10,402 opposed to 11,776) than T. pseudonana and no major synteny (gene order) could
be detected between the two genomes. T. pseudonana genes show an average of ~1.52 introns per gene as opposed to 0.79 in P.
tricornutum, suggesting recent widespread intron gain in the centric diatom.[43][44] 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.[43] Comparative genomics also established that a specific class
oftransposable 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.[45]
Importantly, diatom genomics brought much information about the extent and dynamics of the endosymbiotic gene transfer (EGT)
process. Comparison of the T. pseudonana proteins with homologs in other organisms suggested that hundreds have their closest
homologs in the Plantae lineage. EGT towards diatom genomes can be illustrated by the fact that the T. pseudonana genome
encodes six proteins which are most closely related to genes encoded by the Guillardia theta (cryptomonad) nucleomorph genome.
Four of these genes are also found in red algal plastid genomes, thus demonstrating successive EGT from red algal plastid to red
algal nucleus (nucleomorph) to heterokont host nucleus.[42] More recent phylogenomic analyses of diatom proteomes provided
evidence for a prasinophyte-like endosymbiont in the common ancestor of chromalveolates as supported by the fact the 70% of
diatom genes of Plantae origin are of green lineage provenance and that such genes are also found in the genome of other
stramenopiles. 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.[46] However, phylogenomic analyses of diatom proteomes and chromalveolate evolutionary history will likely take advantage
of complementary genomic data from under-sequenced lineages such as red algae.
In addition to EGT, horizontal gene transfer (HGT) can occur independently of an endosymbiotic event. The publication of the P.
tricornutum genome reported that at least 587 P. tricornutum genes appear to be most closely related to bacterial genes, accounting
for more than 5% of the P. tricornutum proteome. About half of these are also found in the T. pseudonana genome, attesting their
ancient incorporation in the diatom lineage.[43]
Nanotechnology research
The deposition of silica by diatoms may also prove to be of utility to nanotechnology.[47] Diatom cells repeatedly and reliably
manufacture valves of various shapes and sizes, potentially allowing diatoms to manufacture micro- or nano-scale structures which
may be of use in a range of devices, including: optical systems; semiconductor nanolithography; and even using diatom valves as
vehicles for drug delivery. Using an appropriate artificial selection procedure, diatoms that produce valves of particular shapes and
sizes could be evolved in the laboratory, and then used in chemostat cultures to mass produce nanoscale components.[48] It has also
been proposed that diatoms could be used as a component of solar cells, by substituting photosensitive titanium dioxide for the
silicon dioxide normally used in the creation of cell walls.[49]
Slime mold
Slime mold Stemonitis fusca in Scotland,UK
Fuligo septica, the "dog vomit" slime mold
Mycetozoa from Ernst Haeckel's 1904Kunstformen der Natur (Artforms of Nature)
Slime mold (or slime mould, see spelling differences) is a broad term describing fungus-like organisms that use spores to
reproduce.[1]Slime molds were formerly classified as fungi, but are no longer considered part of this kingdom.[2]
Their common name refers to part of some of these organisms' life cycles where they can appear as gelatinous "slime". This is
mostly seen with the myxomycetes, which are the only macroscopic slime molds.
Slime molds have been found all over the world and feed on microorganisms that live in any type of dead plant material. For this
reason, these organisms are usually found in soil, lawns, and on the forest floor, commonly on deciduous logs. However, in tropical
areas they are also common on inflorescences, fruits and in aerial situations (e.g., in the canopy of trees). In urban areas, they are
found on mulch or even in theleaf mold in gutters. One of the most commonly encountered slime molds, both in nature in forests in
the temperate zones of the earth as well as in classrooms and laboratories is the yellow Physarum polycephalum.
Most slime mold are smaller than a few centimeters, but some species may reach sizes of up to several square meters and masses of
up to 30 grams.[3] Many have striking colours such as yellow, brown and white.
Taxonomy
Slime molds can generally be divided into two main groups.

A plasmodial slime mold involves numerous individual cells attached to each other, forming one large membrane. This
"supercell" (asyncytium) is essentially a bag of cytoplasm containing thousands of individual nuclei. See heterokaryosis.

By contrast, cellular slime molds spend most of their lives as individual unicellular protists, but when a chemical signal is
secreted, they assemble into a cluster that acts as one organism.
Slime molds, as a group, are polyphyletic. They were originally represented by the subkingdom Gymnomycota in the Fungi kingdom
and included the defunct phyla Myxomycota, Acrasiomycota and Labyrinthulomycota. Today, slime molds have been divided
between several supergroups, none of which are included in the kingdom Fungi.
In more strict terms, slime molds comprise the group of the mycetozoans (myxomycetes, dictyostelids and protostelids). However,
even at this level there are conflicts to be resolved. Recent molecular evidence shows that the first two groups are likely to be
monophyletic; however the protostelids seem to be polyphyletic, too. For this reason, scientists are currently trying to understand
the relationships among these three groups.
Bikont

Acrasiomycota: slime molds which belong to the super group Excavata as the family Acrasidae. They have a similar life style
toDictyostelids, but their amoebae behave differently and are of uncertain taxonomic position.

Labyrinthulomycota: slime nets which belong to the super group Chromalveolata as the class Labyrinthulomycetes. They are
marine and form labyrinthine networks of tubes in which amoeba without pseudopods can travel.

Plasmodiophorids: parasitic protists which belong to the super group Rhizaria. They can cause cabbage club root
disease and powdery scab tuber disease. The Plasmodiophorids also form coenocytes but are internal parasites of plants (e.g.,
Club root disease of cabbages).
Amoebozoa
Slime mold (Physarum polycephalum)

Mycetozoa, which includes the defunct phylum Myxomycota, belong to the supergroup Amoebozoa and include:

Myxogastria or myxomycetes : syncytial or plasmodial slime molds

Dictyosteliida: unicellular slime molds or dictyostelids.

Protostelids.
The most commonly encountered are the Myxogastria. A common slime mold which forms tiny brown tufts on rotting logs
is Stemonitis. Another form which lives in rotting logs and is often used in research is Physarum polycephalum. In logs it has the
appearance of a slimy web-work of yellow threads, up to a few feet in size. Fuligo forms yellow crusts in mulch.
The Dictyosteliida, cellular slime molds, are distantly related to the plasmodial slime molds and have a very different lifestyle. Their
amoebae do not form huge coenocytes, and remain individual. They live in similar habitats and feed on microorganisms. When food
runs out and they are ready to form sporangia, they do something radically different. They release signal molecules into their
environment, by which they find each other and create swarms. These amoeba then join up into a tiny multicellular slug-like
coordinated creature, which crawls to an open lit place and grows into a fruiting body. Some of the amoebae become spores to
begin the next generation, but some of the amoebae sacrifice themselves to become a dead stalk, lifting the spores up into the air.
The Protostelids have characters intermediate between the previous two groups, but they are much smaller, the fruiting bodies only
forming one to a few spores.
Opisthokont
Fonticula is a cellular slime mold which forms a fruiting body in a volcano shape. [4] Fonticula is not closely related to either the
Dictyosteliida or the Acrasidae.[5] A 2009 paper finds it to be related to Nuclearia, which in turn is related to fungi.[6]
Life cycle
Slime mold growing out of bin of wet paper
They begin life as amoeba-like cells. These unicellular amoebae are commonly haploid and multiply if they encounter their favorite
food,bacteria. These amoebae can mate if they encounter the correct mating type and form zygotes which then grow into
plasmodia. These contain many nuclei without cell membranes between them, which can grow to be meters in size. One variety is
often seen as a slimy yellow network in and on rotting logs. The amoebae and the plasmodia engulf microorganisms. The
plasmodium grows into an interconnected network of protoplasmic strands. [7]
Within each protoplasmic strand the cytoplasmic contents rapidly stream. If one strand is carefully watched for about 50 seconds
the cytoplasm can be seen to slow, stop, and then reverse direction. The streaming protoplasm within a plasmodial strand can reach
speeds of up to 1.35 mm per second which is the fastest rate recorded for any micro-organism.[8] Migration of the plasmodium is
accomplished when more protoplasm streams to advancing areas and protoplasm is withdrawn from rear areas. When the food
supply wanes, the plasmodium will migrate to the surface of its substrate and transform into rigid fruiting bodies. The fruiting bodies
or sporangia are what we commonly see, they superficially look like fungi or molds but are not related to the true fungi. These
sporangia will then release spores which hatch into amoebae to begin the life cycle again. [7]
Plasmodia
The mid sporangial phase ofEnteridium lycoperdon.
In Myxomycetes, the plasmoidal portion of the life cycle only occurs after syngamy, which is the fusion of cytoplasm and nuclei of
myxoamoebae or swarm cells. Therefore, all of the nuclei are diploid at this stage and mitosis occurs simultaneously throughout the
organism. Myxomycete plasmodia are multinucleate masses of protoplasm that move by cytoplasmic streaming. In order for the
plasmodium to move, cytoplasm must be diverted towards the leading edge from the lagging end. This process results in the
plasmodium advancing in fan-like fronts. As it moves, plasmodium also gains nutrients through the phagocytosis of bacteria and
small pieces of organic matter.
The Myxomycete plasmodium also has the ability to subdivide and establish separate plasmodia. Conversely, separate plasmodia
that are genetically similar and compatible can fuse together to create a larger plasmodium. In the event that conditions become
dry, the plasmodium will form a sclerotium, essentially a dry and dormant state. In the event that conditions become moist again
the sclerotium absorbs water and an active plasmodium is restored. When the food supply wanes, the Myxomycete plasmodium will
enter the next stage of its life cycle forming haploid spores, often in a well-defined sporangium or other spore-bearing structure.
In popular culture

Traditional Finnish lore describes how malicious witches used yellow Fuligo (there called "paranvoi," or butter of the familiar) to
spoil milk.

Mycologist Tom Volk reports that the plasmodium of Fuligo is eaten in Mexico.[9]

The webcomic GPF has as main characters two sentient, talking slime molds by the names of Frederick Physarum and
Persephone.

The computer game NetHack has Slime Mold as an edible, re-nameable fruit. This is an homage to the earlier game Rogue,
which featured Slime Molds the adventurer could find and add to inventory/eat. When a slime mold was eaten, the message
displayed was "My, that was a yummy Slime Mold."

The giant amoeba-like alien that terrorizes the small community of Downingtown, Pennsylvania, in the 1958 American
horror/science-fiction film The Blob might be based on slime molds.[10]

The lead character in AMC's series "Rubicon," Will Travers, gives a quick description of slime mold behavior as a dinner topic at
his boss' house in Episode 6.[11
Paramecium
Paramecium
Paramecium aurelia
Scientific classification
Domain:
Eukaryota
Kingdom:
Protista
Phylum:
Ciliophora
Class:
Ciliatea
Order:
Peniculida
Family:
Parameciidae
Genus:
Paramecium
Müller, 1773
Species
Paramecium aurelia
Paramecium bursaria
Paramecium caudatum
Paramecium tarantella
Paramecium is a group of unicellular ciliate protozoa, which are commonly studied as a representative of the ciliate group, and
range from about 50 to 350 μm in length. Simple cilia cover the body, which allow the cell to move with a synchronous motion (like
a caterpillar) at speeds of approximately 2,700μm/second (12 body lengths per second). There is also a deep oral groove containing
inconspicuous compound oral cilia (as found in other peniculids) used to draw food inside. They generally feed on bacteria and other
small cells. Osmoregulation is carried out by a pair of contractile vacuoles, which actively expel water from the cell absorbed
by osmosis from their surroundings.
Paramecia are widespread in freshwater environments, and are especially common in scums. Recently, some new species of
Paramecia have been discovered in the oceans.
Certain single-celled eukaryotes, such as Paramecium, are examples for exceptions to the universality of the genetic code: in their
translation systems a few codons differ from the standard ones.
Physiology
The paramecium approximates a prolate spheroid[1], rounded at the front and pointed at the back. The pellicle is a stiff but elastic
membrane that gives the paramecium its definite shape. Covering the outer edge are hairlike structures, called cilia. On the side,
beginning near the front end continuing down half way, is the oral groove, which collects food until it is swept into the cell mouth.
There is an opening near the back end called the anal pore. The contractile vacuole and its radiating canals — referred to previously
for osmoregulation of the organism, are also found on the outside of a paramecium. The paramecium is very commonly mistaken for
a blepharisma.
The paramecium contains cytoplasm, trichocysts, the gullet, food vacuoles, the macronucleus, and the micronucleus.
Movement
Cilia are the locomotive structures of the paramecium. In order for the paramecium to move forward, its cilia beat at an angle,
backwards in unison (i.e., the cilium wiggles from tip-to-base). This means that the paramecium moves by spiraling through the
water on an invisible axis. The paramecium can also move backwards when the cilia beat forward at an angle in unison (i.e., the cilia
go backward. The paramecium turns slightly and goes forward again. If it runs into the solid object again it will repeat this process
until it can get past the object.
Gathering food
Paramecia feed on microorganisms like bacteria, algae, and yeasts. To gather its food, the paramecium uses its cilia to sweep up
food along with some water into the cell mouth after it falls into the oral groove. The food goes through the cell mouth into the
gullet. When enough food has accumulated at the gullet base, it forms a food vacuole in the cytoplasm, and travels through the cell,
through the back end first. As it moves along, enzymes from the cytoplasm enter the vacuole to digest the contents, digested
nutrients then going into the cytoplasm, and the vacuole shrinks. When the vacuole reaches the anal pore, it ruptures, expelling its
waste contents to the exterior.
Symbiosis
One of the most interesting known symbiotic relationships is that of Paramecium aurelia and its bacterial endosymbionts. See also
the Chlorella symbiosis with Paramecium bursaria.
Genome
The paramecium genome has been sequenced (species: Paramecium tetraurelia), providing evidence for three whole-genome
duplication.[2]
In some ciliates, like Stylonychia and Paramecium, only UGA is decoded as a stop codon, while UAG and UAA are reassigned as sense
codons.[3]
Learning
The question of whether paramecia exhibit learning has been the object of a great deal of experimentation, yielding equivocal
results. In one of the most recent experiments published [4], the authors, by using a voltage as a reinforcement, concluded
that paramecium may indeed learn to discriminate between different brightness levels.