GLOSSARY

Abioticrefers to a non-living part of an ecosystem that shapes its environment. In a terrestrial ecosystem, examples include temperature, light, and water. In a marine ecosystem, abiotic factors would include salinity and ocean currents. Abiotic and biotic factors work together to create a unique ecosystem.

Alveoli –trough-shaped, transapical depressions on the inner side of the valve. Apically, they are delimited by the transapical ribs, and towards the valve edge by one or more rows of areolae. On the inside they are either completely open, or as in many Pinnularia species, partly occluded by an inner wall.

Anisogamyalso called heterogamy is the form of sexual reproduction that involves the union or fusion of two gametes, which differs slightly in size and/or form. The related adjective is anisogamous.

Apex –the summit, the terminus; end of a projection; the upper end of a filament of a cell

Apiculate –having a short sharply pointed tip, unsubdivided, simple, having no divisions or subdivisions.

Araphid –refers to diatoms that are pennate and lack a raphe system. Examples of araphid genera include Diatoma, Fragillaria and Synedra.

Asexual reproduction –A type of reproduction which doesn’t involve the fusion of gametes or change in chromosome number. Diatoms reproduce asexually by cell division to produce two daughter cells by mitosis; each daughter cell receives one valve and is reproduced by furrowing. The cell has vesicles that increase the deposition of silica creating a new valve girdle band.

Asymmetrical –having parts that fail to correspond to one another in shape, size, or arrangement; lacking in symmetry.

Autotroph –or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins using carbon from simple substances such as carbon dioxide, generally using energy from sunlight (photosynthesis) or inorganic chemical reactions (chemosynthesis).

Automated cell counter –is a machine that automatically counts cells. The sample is loaded into an automated cell counter, and it is forced through a small tube while the automated cell counter uses optical or electrical impedance sensors to count how many cells go through the tube.

Auxosporea specialized reproductive cell in diatoms produced at a key stage in the cell cycle or life history, usually resulting from the union of two smaller cells or their contents and associated with rejuvenescence in cells that have become progressively smaller because of repeated divisions. It typically plays a role in growth processes, sexual reproduction or dormancy.

Bifurcate –refers to a structure that divides from one branch into two branches. The term is used to describe the branching of the distal raphe fissure of some diatoms. For example, the distal raphe fissure is bifurcate in the genus Muelleria.

Bilateral symmetry –refers to organisms with body shapes that are mirror images along a midline called the sagittal plane. The internal organs, however, are not necessarily distributed symmetrically. Diatoms have two distinct shapes: a few (centric diatoms) are radially symmetric, while most (pennate diatoms) are broadly bilaterally symmetric.

Binary fission –Division of a cell into two parts. Diatoms primarily reproduce asexually via binary fission. Each daughter cell receives one of the frustules from the parent cell, which forms the larger frustules, and provides the basis for the construction of the second, slightly smaller frustules. Since, the two frustules are not the same size, with each replication, one daughter cell will be slightly smaller than the other.

Biodiversity –is a term used to describe the enormous variety of species of living things on earth. Biodiversity is the shortened form of two words “biological” and “diversity”. It can be used more specifically to refer to all of the species in one region or ecosystem. Biodiversity boost ecosystem productivity where each species, no matter how small, all have an important role to play. Greater species diversity ensures natural sustainability for all life forms.

Biofuelany fuel that originates from biomass, that is, plant or algal material or animal waste which energy is derived from biological carbon fixation. Biofuel is a source of renewable energy, unlike fossil fuels such as petroleum, coal, and natural gas.

Biotic - describes a living component of an ecosystem; for example, organisms, such as plants and animals, that is, all living things.

Biraphiddescribes diatoms with a raphe on each valve. Examples of biraphid genera include—Navicula, Amphora, Gomphonema and Mastogloia.

Brackish water –is water occurring in natural environment with salinity levels between seawater and freshwater. It may result from mixing seawater with freshwater together, as in estuaries.

Buoyancy –is the force that causes objects to float. It is the force exerted on an object that is partly or wholly immersed in a fluid. Buoyancy is caused by the differences in pressure acting on opposite sides of an object immersed in a static fluid.

Canaliculus (plural canaliculi) - a tube-like narrow channel or passageway which runs through the valve surface of diatoms.

Capitate –describes a valve end, or apex, as having the shape of a head, or the shape of a rounded knob. Similar term for valve end includes sub capitate (less strongly capitate. In general, capitates and sub capitate ends are more expanded than the narrowest points on the valve.

CarotenesOrange-yellow plant photosynthetic pigments found in the chloroplasts and other plastids of which there are four kinds in algae. They absorb ultraviolet, violet, and blue light and scatter orange or red light and yellow light.

Central nodule –a central nodule is the thickly silicified area located at the centre or central area, between the proximal raphe ends in raphid diatoms. It is often thickened in both valve and girdle views. It is the site where silica deposition vesicle deposits the first silica during valve formation.

Centralesan order of diatoms, with radially symmetrical cells in valve view, mostly marine and pelagic; cell form is often circular and always lacking a raphe or pseudoraphe and having radial markings and often spines.

Chemostatis a bioreactor to which fresh medium is continuously added, while culture liquid containing left over nutrients, metabolic end products and microorganisms are continuously removed at the same rate to keep the culture volume constant.

Chloroplast –a pigment contained organelle of plant and algal cells that carries out photosynthesis, the process of converting light energy to energy stored in the form of sugar and other organic molecules that the plant or alga uses as food. Chloroplasts are double membrane-bound organelles containing elaborate membranous sacs known as thylakoids; the membranes contain chlorophyll a, and other components of the photosynthetic light reactions.

Cholesterol –a compound of the sterol type found in most tissues. Cholesterol and its derivatives are important constituents of cell membranes and precursors of other steroid compounds.

Chromatophore –a coloured plastid containing one or more pigments including chloroplasts.

Chromoplast –a plastid, heterogeneous organelle responsible for pigment synthesis and storage in specific eukaryotes. It is thought that like all other plastids including chloroplasts and leucoplasts they are descended from symbiotic prokaryotes.

Cinguluma cingulum (plural cingula) is the series of siliceous linking bands associated with a diatom (dinoflagellate) valve. Each band is called a girdle band, or copula. A cingulum and its attached valve make up a theca.

Clavaterefers to an object having the shape of a club. Clavate is usually used to describe the asymmetry of Gomphoneis and Gomphonema in valve view.

Commensalismin biology is a relationship between individuals of two species in which one species obtains food or other benefits from the other without either harming or benefiting the latter. The commensal, that is, the species that benefits from the association may obtain nutrients, shelter, support, or locomotion from the host species, which is unaffected. Example is between the tube-building species of the genus Cymbella and Nitzschia dissipata, both freshwater diatoms.

Concave –hollowed out like a saucer; having the outline or surface that curves inwards like the interior of a circle or sphere. It describes shapes that curve inward. In geometry, it is a polygon with one interior angle greater than 180o.

Convergent –refers to leaning towards a point, e.g., the central nodule, with the sternum as the origin. Convergent striae may occur throughout the valve, at the valvar centre, or at the valve apices. In contrast, striae are radiate, or divergent, when they lean away from the central nodule, with the sternum as the origin.

Convexhaving the outline or surface curved like the exterior of a circle or sphere. It describes a shape or line that curves outward, and its middle is thicker than its edges. It also used in geometry, where it describes a polygon with interior angles less than or equal to 180o.

Cosmopolitan –in biogeography, a taxon is said to have a cosmopolitan distribution if its range extends across all or most of the world in appropriate habitats. Such a taxon, usually a species, is said to exhibit cosmopolitanism or cosmopolitism.

Costarefers to a thickening parallel to the striae. The plural is costae. It is an unornamented, elongated thickening of the valve.

Cribrum (plural cribra)—A cribrum is a type of velum that is reticulate or that has regularly arranged pores. Cribra may be flat or domed. In some genera they may be visible with LM but are usually visible only with electron microscopy. Domed cribra are characteristic of the Thalassiosirales.

Crysolaminarina storage polysaccharide typically found in photosynthetic heterokonts. It is used as carbohydrate food reserve by phytoplankton such as Bacillariophyta.

Cytokinesisis the physical process of cell division, which divides the cytoplasm of a parental cell into two daughter cells. It occurs concurrently with two types of nuclear division called mitosis and meiosis.

Diatomaceous earth –also known as diatomite or kieselgur, is a naturally occurring, soft, siliceous sedimentary rock consisting of fossilized remains of diatoms crumbled into a fine white to off-white powder. It has a particle size ranging from less than 3µm to more than 1mm, but typically 10 to 200µm.

Diatomaceous Earth filter –referred to as DE filters are simple and effective filters in removing cysts, algae, and asbestos from water. DE has been employed in many food and beverage applications and used specifically to filter domestic potable water supply.

Diatomitealso known as diatomaceous earth is the naturally occurring fossilized remains of diatoms. They belong to the class of golden-brown algae known as Bacillariophyceae. Diatomite is a near pure sedimentary deposit consisting almost entirely of silica.

Diatom mucilage –refers to a polysaccharide substance in form of threads or strands that brings about cell-substratum adhesion at the raphe and provides the tractive driving force for diatom gliding, a special form of motility observed in raphid diatoms. The mucilage strands have a significant influence on biofilm formation processes.

Digital flow cytometry –is an electric flow cytometry (FC) where the pulse is converted to a digital number via the analog-to-digital converter (ADC). The resultant digital number is transferred to the computer and analyzed to detect and measure physical and chemical characteristics of a population of cells or particles. In this process, a sample containing cells or particles is suspended in a fluid and injected into the flow cytometer instrument.

Dorsiventralrefers to an organ that has two surfaces differing from each other in appearance and structure. This term has also been used as a synonym for dorsiventral organs, those that extend from a dorsal to a ventral surface.

Dystrophic –used in ecology to describe a lake having too low an accumulation of dissolved nutrients to support abundant plant life; having highly acid, brownish waters filled with undecayed plant materials, and eventually into a peat or marsh.

Eicosapentaenoic acid (EPA)—is one of several omega–3 fatty acids found in cold water fatty fish, such as salmon. Omega–3 fatty acids are part of a healthy diet that helps lower risk of heart diseases.

Electron Microscopy (EM) —is a technique for obtaining high resolution image of biological and non-biological specimens. It is used in biological and biomedical research to investigate the detailed structure of tissues, cells, organelles and macromolecular complexes.

Elliptical –the adjective that describes the shape of an ellipse, which is an elongated circle, stretched into an oval tapering at each end.

Endozoic— Adjective used in botany to describe two scenarios: 1. (of a plant) living within an animal 2. Denoting seed dispersal in which the seed are swallowed by an animal and subsequently pass out in the faeces.

Epibenthic –refers to organisms that live on or just above the bottom sediments in a body of water. These organisms tend to forage on the creatures that live in or on the sediments.

Epilithic diatoms—refers to diatoms that grow on rock substrates, and may include associations of attached, motile, epiphytic algae (attached to algal filaments) and facultative planktonic taxa.

Epilithonan epilithon is the community of organisms within the slimy layer that develops on the surfaces of stones in aquatic habitats.

Epipelic—refers to the growth habit of algae living on mud (sediments, clays, and silt), in other words, residing at the interface of water and sediment.

Epipelonrefers the Cyanobacteria and eukaryotic algae that live on or in association with fine-grained substrata or sand.

Epiphytic –refers to an organism that grows on the surface of a plant but does not feed from it. It derives its moisture and nutrients from the air, rain, water or from debris accumulating around it.

Epiphytonis a biofilm that grows on the stems and leaves of aquatic plants, consisting of assemblages of algae, diatoms, bacteria, and extracellular polymeric substances (EPS).

Episalmicrefers to algae attached to sand.

Epitheca –is the larger half of a frustule. The epitheca overlaps the hypotheca.

Epivalve –in the anatomy of the diatom, the valve of the epitheca is called the epivalve and the girdle elements (cincture or pleura are named the epicingulum.

Estuarine –a coastal ecosystem or habitat where salt water from the ocean typically mixes with fresh water from rivers or streams.

Eukaryote –an organism in which the cells have a clearly defined nucleus enclosed by a membrane, along with organelles (small, self-contained cellular parts that perform specific functions). Chromosomes are contained within the cell nucleus. Eukaryotes are generally considered to be more advanced forms of life than prokaryotes.

Eutrophic— is a water body having the highest amount of nutrients and biological productivity. The water is said to be of “poor” quality for human consumption. The “Trophic State Index” (TSI) rating is 60–100. The quantities of nitrogen, phosphorus, and other biological useful nutrients are the primary determinants of a water body’s TSI.

Eutrophicationis the process in which a water body becomes overly enriched with nutrients, leading to plentiful growth of simple plant life. The excessive growth or blooms of algae in a water body are indicators of this process.

Extracellular polysaccharide –also referred to exopolysaccharide (EPS) is a high-molecular weight sugar-based polymer that is synthesized and secreted by many microorganisms including diatoms. It is of important nutritive value in atypical conditions.

Filiform –describes diatoms or objects that have the shape of a thread.

Flagellum –a slender lash-like appendage that protrudes from the cell body of certain organisms, that enable such cells (protozoa, protists, bacteria, spermatozoa, etc. to swim.

Foramen –is a large opening in one wall of a loculate areola. It is located on the external or internal wall of the areola, depending on the species, opposite the velum. The plural is foramina.

Freshwater - a subset of the Earth’s aquatic ecosystems of naturally occurring water found in lakes, ponds, rivers, streams, springs, bogs, wetlands, and underground as water having low concentrations of dissolved salts.

Frustule –is the hard and porous cell wall or external layer of diatoms. The frustules are composed almost purely of silica, made from silicic acid, and is coated with a layer of organic substance, referred to in earlier literature on diatoms as pectin, a fibre most commonly found in cells.

Fucoxanthinis xanthophylls that contribute more than 10% of the estimated total production of carotenoids in nature. It is an accessory pigment found in the chloroplasts of many brown algae, such as Fucus spp., and the golden-brown unicellular microalgae, the diatoms.

Fultoportula—is a process consisting of a central tube passing through the valve and two or more satellite pores that surround and support the central tube. Externally the fultoportula appears as either a tube, or a simple pore in the valve wall. Internally, the satellite pores are visible. The plural is fultoportulae. These processes are found only in the centric order Thalassiosirales. In Latin, the meaning is “strutted opening”.

Genomeis an organism’s complete set of genetic instructions. Each genome contains all the information needed to build that organism and allow it to grow and develop.

Gibbous –refers to part of a valve outline that is convex, rounded, or protuberant. A gibbous outline exceeds a semi-circle but is less than a circle.

GirdleGirdle view refers to the orientation of frustule such that the mantle of each valve and the girdle bands are closest to the observer.

Global warming –is the long-term heating of Earth’s climate system observed since the pre- industrial period due to human activities, primarily fossil fuel burning, which increases heat- trapping greenhouse gas levels in Earth’s atmosphere.

Golgi bodyalso known as Golgi apparatus, is a cell organelle that helps process and package proteins and lipid molecules, especially proteins destined to be exported from the cell. The plural is known as Golgi bodies, and they appear as a series of stacked membranes.

Haemocytometeris a counting-chamber device originally designed and usually used for visual counting of cells in a blood sample or other fluid under the microscope. The haemocytometer was invented by Louis-Charles Malassez and consists of a thick glass microscope slide with a rectangular indentation that creates a precision volume chamber.

Heterokonts –refers to organisms with two flagella of unequal lengths. A group of protists (formally referred to as Heterokonta, Heterokontae or Heterokontophyta). The group is a major line of eukaryotic algae ranging from the giant multicellular kelps to the unicellular diatoms, which are a primary component of plankton.

Heteropolar –describes valves in which the poles, or apices, of the apical axis have different shapes. Heteropolar valves are asymmetric to the transapical axis. Examples of genera include Gomphoneis and Gomphonema.

Heterotroph –also called mixotroph refers to organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary, and tertiary consumers, but not producers.

Heterotrophic –adjective describing organisms requiring complex or organic compounds of nitrogen and carbon (such as that obtained from plant and animal matter) for metabolic synthesis.

Hexagonal –refers to the intricate hexagonal lattice of pores on the diatom surface that encompasses areolae (hexagonal or polygonal boxlike perforation with a sieve present on the surface of a diatom.

Horizontal axis –a horizontal line is one which runs from left to right across a side. It comes from the word “horizon”, in the sense that horizontal lines are parallel to the horizon. The horizon is horizontal. Its cousin is the vertical line which runs up and down the folio.

Hyaline –refers to any area of a diatom valve that is unornamented, that is, it lacks pores or other structures.

Hypotheca –refers to the smaller half of a frustules. The hypotheca is overlapped by the epitheca. In Greek hypotheca means inner sheath.

Isogamy –is a form of sexual reproduction that involves gametes of similar morphology (generally similar in shape and size), found in most unicellular organisms. Because the gametes are alike, they generally cannot be classified as male and female. Instead, they are noted as plus (+) and minus (-) strains.

Isopolardescribes valves in which the poles, or apices, of the apical axis are similar in size and shape. Isopolar valves are symmetric to the transapical axis.

Keel –is a thickening of silica that contains the raphe within a canal. The keel elevates the raphe from the surface of the valve, allowing maximal contact of the raphe with surfaces of motility. Several diatom genera possess a keel, including Nitzschia, Iconella and Entomoneis.

Lanceolate –refers to a valve having an elongated outline, widest at the middle and tapering to both ends. The valve width may range from wide to narrow.

Lentic - which means slow or motionless, refers to environments of standing waters such as lakes and ponds (lacustrine), or swamps and marshes (paludal).

Leucoplasts –are a group of plastids that include many differentiated colourless organelles with very different functions (e.g., amyloplasts), which act as storage for starch in non-green tissues.

Life cycle –Individual cells range in size from 2 to 200 µm. In the presence of adequate nutrients and sunlight, an assemblage of living diatoms doubles approximately every 24 hours by asexual multiple fission; the maximum life span of individual cells is about six days.

Light Microscopy (LM)—a process that employs an instrument that uses visible light and magnifying lenses to examine small objects not visible to the naked eye, or in finer detail than the naked eye allows.

Limnetic Zone –is the open and well-lit area of a free-standing body of freshwater, such as a lake or pond. Not included in this area is the littoral zone, which is the shallow, near-shore of the water body. Together, these two zones comprise the photic zone.

Littoral zone –refers to the marine ecological realm that experiences the effects of tidal and longshore currents and breaking waves to a depth of 5 to 10 metres (16 to 33 feet) below the low-tide level, depending on the intensity of storm waves.

Loculate –refers to an object having a locule, or chamber. A loculate valve has loculate areolae. A loculate areola is made of a chamber with a velum and a foramen for two of its walls.

Longitudinal canal –is a chamber with the shape of a tube inside the valve, orientated along the apical axis. The canals appear as longitudinal lines and may be central or marginal.

Longitudinal rib –is a solid silica structure that runs along each side of the raphe in genera such as Frustulia.

Lotic –refers to environments of running water (fluvial or fluviatile) habitats such as rivers and streams.

Macrophytesaquatic plants that have adapted to living in aquatic environments (saltwater and freshwater). They are also referred to as hydrophytes to distinguish them from algae and other microphytes. A macrophyte is a plant that grows in or near water and is either emergent, submergent, or floating. In lakes and rivers macrophytes provide cover for fish, substrates for aquatic invertebrates, produce oxygen, and act as food for some fish and wildlife. They are primary producers and are the basis of the food web for many organisms. Marinerefers to habitats or environments that support oceanic life and is circumscribed in some way by the level of saltwater that is in the sea. Marine habitats can be divided into

coastal or open ocean habitats.

Mixotroph –see heterotroph

Mutualism –describes the ecological interaction between two or more organisms of different species where each species has a net benefit. Examples are interactions between bacteria and diatoms where many bacteria produce B12, thus providing a source for diatoms. In return the bacteria would benefit from dissolved organic matter (DOM) produced by the diatoms.

Nanoscale –is the nanoscopic scale usually refers to structures with a length scale applicable to nanotechnology, usually cited as 1–100 nanometres. A nanometre is a billionth of a metre. Nanotechnology –is science, engineering, and technology conducted at the nanoscale, which is about 1 to 100 nanometres. Nanoscience and nanotechnology are the study and application of

extremely small things and can be used across all the other science fields, such as chemistry, biology, physics, materials science and engineering. Nanotechnology, also shortened to

nanotech, is the use of matter on an atomic, molecular, and supramolecular scale for industrial purposes.

Neritic –relating to or denoting the shallow part of the sea near a coast and overlying the continental shelf where light penetrates to the sea floor. Due to the abundant supply of sunlight and nutrients in this zone, it is the most productive ocean zone supporting most of the marine life.

Oceanic –is typically defined as the area of the ocean lying beyond the continental shelf, but operationally is often referred to as the beginning where the water depths drop to below 200 metres seaward from the coast into the open ocean.

Ocellusis a porefield that has a distinct hyaline rim between its pores and the areaolae. Plural is ocelli. Ocelli are found in polar centric genera such as Pleurosiri and Eupodiscus.

Oligotrophic –is a trophic state index designed to rate water bodies based on the amount of biological productivity they sustain. Oligotrophic water, with a TSI 0–40, has the least amount of nutrients and biological productivity. It is referred to as “good” water quality for human consumption. The quantities of nitrogen, phosphorus, and other biologically useful nutrients are the primary determinants of a water body’s TSI.

Oogamyis the familiar form of sexual reproduction. It is a type of heterogamy in which the female gamete, the egg cell, is significantly larger than the male gamete and is non-motile. The male gametes are typically highly motile and are usually tasked with all the movement necessary to bring the respective gametes together for union.

Pantonematicdescribes a type of flagellum with two rows of hairs or fibrils but no terminal fibril.

Parasitism –is a symbiotic relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. Examples of algal parasitism is between the fungus Olpidium phycophagum, an encysted parasite, found in the diatom Eucampia zoodiacus.

PennalesThe order Pennales is a traditional subdivision of the heterokont algae known as diatoms. The order is named for the shape of the cell walls of pennate diatoms, which are elongated in valve view. The valves may be linear or oval, and usually bear bilaterally symmetrical ornamental patterns.

Pervalvar –describes the axis of the valve which is perpendicular to the centre of the valve face. In centric diatoms, the centre is the meeting point of the radii. In pennate diatoms, the centre is the meeting point of the apical and transapical axes.

Photomicrography—in biology, photography of biological materials, which may be killed, dyed so that their structure can be seen, and mounted on glass slides for photographing by transmitted light using ordinary light microscopes; or by using ultraviolet, infrared, electron, or x-ray microscopes, sharp photographs can be made of living unstained specimens.

Photosynthesis –the process by which green plants and certain other organisms including diatoms transform light energy into chemical energy. During photosynthesis in plants, light energy is captured and used to convert water, carbon dioxide, and minerals into oxygen and energy-rich organic compounds.

Photosystems –are functional and structural units of protein complexes involved in photosynthesis. Together they carry out the primary photochemistry of photosynthesis: the absorption of light and the transfer of energy and electrons. There are two types of photosystems: PSI and PSII.

Phylogenetics –is the study of evolutionary relationships among biological entities—often species, individuals or genes which may be referred to as taxa.

Phytoplanktonare the free-floating autotrophic microscopic components of the plankton community and key part of ocean and freshwater ecosystems.

Planktonic –describes organisms including protists, microorganisms, and certain types of small metazoans, all sharing a common liability to passive entrainment in water currents, generated by tide, wind, convection, gravity, and the rotation of the earth.

Plastid –a plastid is the pigmented organelle that is the site of photosynthesis. Plastids contain carotenoid pigments such as beta-carotene, diatoxanthin, diadinoxanthin and fucoxanthin. Most diatom plastids appear golden brown because the carotenoid pigments mask the colour of the chlorophylls.

Polar nodulerefers to a thick wall on either both the ends of the cell where it projects into the cell interior as a knob and has small pores which connect it with adjacent cell structure.

Polysaccharide –is a large molecule made of many smaller monosaccharides. Monosaccharides are simple sugars, like glucose. Special enzymes bind these small monomers together creating large sugar polymers. A polysaccharide is also called a glycan.

Polyunsaturated fatty acids (PUFAs)—are fatty acids that contain more than one carbon - carbon double bond in their backbone. This class includes many important compounds, such as essential fatty acids and those that give drying oils their characteristic property.

Porefield –is an area of fine pores set apart from the pattern on the rest of the valve. Diatoms excrete mucopolysaccharides through the porefield. These extra polymeric substances (EPS} comprise the stalks and pads which attach diatoms to substrates and to sibling cells. There are several types of porefields.

Pores –special slits or holes found in diatom frustules that provide the diatom access to the external environment for processes such as waste removal and mucilage secretion. The microstructural analysis of the frustules shows that the pores are of various sizes, shapes, and volume.

Pseudoraphe –a clear area on the valve between striae or costae, found on the frustules of some pennate diatoms. The pseudoraphe is called the “central sternum” by some authors.

Punctate –is a type of areola important in diatom taxonomy. An areola is one of the pores in a row that forms a stria on a valve. Some examples of different types of areolae include lineolate (Navicula),, punctuate (Gomphoneis) and loculate (Diploneis)

Pyknotic –describes the irreversible condensation of chromatin in the nucleus of a cell undergoing necrosis or apoptosis in the process of pyknosis. It is followed by karyorrehexis, or fragmentation of the nucleus. Pyknosis is also observed in the maturation of erythrocytes (red blood cells).

Pyrenoids –are sub-cellular micro-compartments found in chloroplasts of many algae. Pyrenoids are associated with the operation of a carbon-concentrating mechanism (CCM). Their main function is to act as centres of carbon dioxide (CO2) fixation, generating and maintaining a CO2 rich environment around the photosynthetic enzyme ribulose–1,5- biphosphate carboxylase/ oxygenase (RuBisCO).

Radial symmetry –is the arrangement of body parts around a central axis, like rays on a sun or pieces in a pie. Diatoms have two distinct shapes: a few (centric diatoms) are radially symmetric, while most (pennate diatoms) are broadly bilaterally symmetric.

Raphe –an elongated groove, fissure, or opening, or a pair of such fissures in the valve of certain pennate diatoms, typically marks the line where two halves are fused.

Rhombic –describes an object that has the shape of a rhombus

Rimoportula –is a tubular process through the valve of some diatoms. On the internal valve face, the rimoportula opening has the shape of a pair of lips. On the external valve face, the rimoportala opening may be a simple, round aperture at the valve surface or it may be a tube extending out from the valve. Plural form is rimoportulae. Rimoportulae are found in centric diatoms, and they extrude polysaccharides and other carbon compounds.

Ringleisteis an internal, silica ledge that projects into the cell interior from the collum. The ringleiste is found only in the genus Aulacoseira and is variously developed in different species of the genus.

Rostrate –describes a valve end having the shape of a beak, or rostrum. Subrostrate end in contrast is less strongly rostrate and may be described as similar to rostrate. Compared to capitate and subcapitate ends, rostrate and subrostrate ends are not more expanded than the narrowest point.

Salinityis the dissolved salt of a body of water. It is a strong contributor to conductivity and total dissolved solids and helps determine many aspects of the chemistry of natural waters and thebiological processes within them.

Scanning electron microscopy (SEM) –a type of electron microscopy that produces images of a sample by scanning the surface with a focused beam of electrons. The electrons interact with atoms in the sample, producing various signals that contain information about the surface topography and composition of the sample. Some SEMs can achieve resolutions better than 1 nanometer.

Sedgewick Rafter Counting Chamber –a premium counting cell chamber designed specifically for the quantitative measurement of the exact number of particles in a precise volume of a fluid.

Septum –is a silica sheet extending internally from the walls of a copula, or girdle band, occluding a portion of its length. By contrast, a septum is part of a copula, while a pseudoseptum is part of a valve. The plural is septa. Septa are found in several genera such as Tabellaria.

Sessile –in biology, sessile describes an organism lacking in self-locomotion. Such an organism is attached directly by its base without a stalk or peduncle. Sessile organisms can move via external forces, such as water currents, but are usually permanently attached to something.

Seta –is a simple or robust extension of the diatom valve. The plural is setae. Setae are more elongate than spines and are found in the genera Chaetoceros and Bacteriastrum. They join frustules together to form chains and maintain the buoyancy of colonies in a planktonic environment.

Silicic acid –a compound (Si(OH)4) of silicon, oxygen, and hydrogen, regarded as the parent substance from which is derived a large family—the silicates—of minerals, salts, and esters. Diatoms require silicic acid to produce their shells made of biogenic silica (bSiO2). Biogenic silica provides diatoms ballast, but cells can remain buoyant due to changes in the cellular constituents which are controlled by metabolic processes.

Solar Panel –is an assembly of photo-voltaic cells mounted in a framework for installation. Solar panels also referred to as photo-voltaic modules, use sunlight as a source of energy and generate direct current electricity to electrical equipment.

Solitary –describes organisms in which all individuals live independently and have all the functions needed to survive and reproduce. Colonies on the other hand, are composed of two or more solitary individuals to be modular.

Spine –a pointed silica extension of the valve, shorter than a seta. Spines may be solid or hollow, very long or tiny, single or many and they may arise from different points on the valve face in different taxa.

Stellate - refers to an object having the shape of a star or having similar parts radiating from a common centre. For example, cells of the genus Asterionella form stellate colonies.

Stremenopileis a clade of organisms distinguished by the presence of stiff tripartite external hairs. In most species, the hairs are attached to flagella. Stremenopile lineage of life are eukaryotes and are single-celled and the group includes a variety of algal protists.

Stria –is a row of areolae, alveoli, or is a single alveolus when the alveolus extends from the apical axis to the margin. The plural is striae. In centric diatoms, striae are usually orientated along radii of a valve. In pennate diatoms, striae are usually oriented on the valve transapically. In Latin, stria means groove or stripe. The different features of striae are important in diatom taxonomy and phylogeny, such as density, orientation, chambering and seriation.

Symbiont –organism living in symbiotic association with another.

Symbiosismeaning living together, is any type of close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic. Living diatoms, for example, Fragilariopsis curta is a common diatom found inside sponges.

Taxon –a taxon, (plural taxa), is a group of one or more populations of an organism or organisms used in the science of biological classification by taxonomists to form a unit. A taxon is usually known by a particular name and given a particular ranking. Taxa are arranged in a hierarchy from kingdom to subspecies or given. In the classification of protists, plants, and animals’ certain taxonomic categories are universally recognized, in descending order; these are kingdom, division (in animals, phylum), class, order, family, genus, species, and subspecies, or race. Rules in for naming the various taxa are in the province of biological nomenclature.

Terrestrialrefers to numerous taxa of diatoms that can survive and reproduce in a variety of terrestrial ecosystems such as soils, mosses, wet walls and rocks in contrast to diatoms generally regarded as inhabitants of water bodies.

Thecarefers to the overlapping sections of diatom frustules known as thecae (or less formally as valves). The joint between the two thecae is supported by bands of silica, girdle bands, that hold them together.

Thermal spring –also known as hot spring, hydrothermal spring, or geothermal spring, is a spring produced by the emergence of geothermally heated groundwater that rises from the Earth’s crust.

Transapical axis - is the short axis of the valve surface of a pennate diatom, passing across the middle of the face perpendicular to the apical axis.

Transmission electron microscopy (TEM)—is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. Transmission electron microscopy is capable of imaging at a significantly higher resolution than light microscopy, owing to the smaller wavelength of electrons.

Triangular diatomsDiatom morphology varies. Although the shape of the cell is usually circular, some cells may be triangular, square, or elliptical.

Trophic level –of an organism is the position it occupies in a food web. A food chain is a succession of organisms that eat other organisms and may, in turn, be eaten themselves. The trophic level of an organism is the number of steps it is from the start of the chain.

Undulatedescribes a feature as having the shape of a wave, with crests and troughs. A valve may be undulate on the margins or on the face.

Vacuole –in biology, is a space, a membrane bound organelle within a cell that is empty of cytoplasm. Vacuoles are closed sacs, made of membranes with inorganic or organic molecules inside, such as enzymes. They have no set shapes or size, and the cell can change them as needed. They are found in most eukaryotic cells and do many things. In plant cells, vacuoles help maintain water balance.

Valve –is the siliceous unit at one end of a frustules. Two opposite valves and their linking girdle bands form a frustule.

Valve mantle –is the downturned side of the valve surrounding the valve face. The mantle is visible when a frustule is viewed in girdle view.

Valve view –refers to the orientation of a frustules such that the valve face is closest to the observer (see also girdle view).

Velumis a thin, porous layer of silica occluding an areola. Electron microscopy is needed to resolve its structure. The plural is vela. In a loculate areola, the velum may form the external or internal wall opposite the foramen, depending on the species.

Volutin –a granular basophilic substance containing nucleic acids that is found especially in cells of microorganisms and is believed to function as a phosphate reserve.

Xanthophylls –a class of oxygen-containing yellow carotenoid pigment, that occurs widely in nature and form one or two major divisions of the carotenoid group; the other division is formed by the carotenes. They are classified as accessory pigments which absorb the wavelength that chlorophyll cannot absorb. They serve as a protection to excessive amount of sunlight to prevent further damage in the cell.