Glossary

Alkaline earth carbonate
Natural alkaline eath carbonates common in the sedimentary realm include the minerals aragonite, calcite, dolomite, magnesite
Aliphatic hydrocarbons
Any chemical compound belonging to the organic class in which the atoms are not linked together to form a ring. They are divided into three main groups according to the types of bonds they contain: alkanes, alkenes, and alkynes. Alkanes (n-alkanes) have only single bonds and a continuous chain structure, alkenes contain a carbon-carbon double bond, and alkynes contain a carbon-carbon triple bond. Aromatic hydrocarbons are classified as either arenes, which contain a benzene ring as a structural unit, or non-benzenoid aromatic hydrocarbons, which are char-acterized by stability in burial but lack a benzene ring as a structural unit.
Anaerobes
Organisms that do not require oxy-gen for growth and may even die in its presence. Obligate (or strict) anaerobes are unable to live in even low oxygen concentrations. Facultative anae-robes are able to live in low or even normal oxygen concentration as well. All anaerobes are simple microorganisms such as bacteria, archaea and some fungi. Archaea are usually strict anaerobes.
Autotrophs
(literally “self-feeders”) are organisms capable of producing organic compounds from simple inorganic compounds.
Basinwide evaporites
Are one of the two major styles of ancient marine-fed salt accumulations known as: (1) marine-fed basinwides and (2) mar-ine-fed platform evaporites. Neither setting is active anywhere on the world’s current land surface. Basinwide salt fills tend be thick (>100 m) and relatively pure with deposits accumulating rapidly across time frames of less than one million years. Basinwide evaporites are most likely to accumulate on the floors of isolated sub-sealevel depressions at times of close proximity of drifting landmasses
Catabolism
The breakdown in living organisms of more complex substances into simpler ones together with a release of energy.
Cellulolytic bacteria
ecompose cellulose; proteolytic bacteria breakdown proteins into simpler, soluble substances such as peptides and amino acids; saccharolytic bacteria breakdown sugars, while homoacetogens are obligately anaerobic bacteria that make acetate from either (H2 + CO2) or from the fermentation of sugars.
Chemoautotrophs
Chemoautotrophs use endogenous light-independent reactions to obtain energy, these reactions involve inorganic molecules and an electron donor other than water and do not release oxygen.
Chemocline
A chemocline is a cline (slope) caused by a strong, vertical chemistry gradient within a body of water. A chemocline is similar to a thermocline.
Chemosynthesis
Synthesis of organic compounds by bacteria or other living organisms using energy derived from reactions involving inorganic chemicals, typically in the absence of sunlight.
Chemoautotrophs
Chemoautotrophs use endogenous light-independent reactions to obtain energy, these reactions involve inorganic molecules and an electron donor other than water and do not release oxygen.
Cyanobacteria
A division of microorganisms that are related to the bacteria but are capable of photosynthesis. They are prokaryotic and represent the earliest known form of life on the earth In the past they have been wrongly classified as blue-green alga
Cyanobacterial toxins
Intoxication of lesser fla-mingo flocks by cyanobacterial toxins, and some-times even mass fatalities have occurred in nearby Lake Bogoria when the birds ingest detached cyanobacterial cells from cyanobacterial mats flourishing in the vicinity of hot springs (Krienitz et al., 2003). This is because the flamingos feeding at night on plankton blooms in a saline lakes need to drink fresh or brackish water after feeding, and to wash their feathers daily. They tend to do this in waters in the vicinity of the hot springs, where salinities are lower than in the main waterbody of the lake where they have been feeding. Mycosystin heptatoxins can characterize the benthic microbial community in those hot spring mats and waters can be dominated by the potentially toxic cyano-bacterial association of Phormidium terebriformis, Oscillatoria willei, Spirulina subsalsa and Synechococcus bigranulatus.
Denitrification
The microbial process by which nitrates are removed from an aqueous liquid
Dissimilatory metabolic processes
Drive the conversion of food or other nutrients into products plus energy-containing compounds
Dissimilatory sulphate reduction.
Sulphate-reducing bacteria gain energy for cell synthesis and growth by coupling the oxidation of organic com-pounds or molecular hydrogen to the reduction of sulphate to sulphide (H2S, HS). This process is called “dissimilatory sulphate reduction”, to allow clear differentiation from assimilatory sulphate reduction. Assimilatory sulphate reduction generates reduced sulphur for biosynthesis (e.g. of cysteine). It is a widespread biochemical capacity in prokaryotes and plants and does not lead to the excretion of sulphide. Only upon decay (putrefac-tion) of the biomass is the assimilated reduced sulphur released as sulphide.
El Niño
Is an abnormal weather pattern caused by the warming of the Pacific Ocean near the equator, off the coast of South America. The sun warms the water near the equator, which can make more clouds and, therefore, more rain. However, normally there are trade winds, which blow that warm water west. During El Niño, those trade winds weaken, or even reverse, which lets the warm water that is usually found in the western Pacific remain or flow east. This warm water displaces the cooler water that is normally found near the surface of the eastern Pacific, setting off atmospheric changes that affect weather patterns in many parts of the world.
Endosymbiosis
Symbiosis in which one of the symbiotic organisms lives inside the other
Endorheic
(also spelled endoreic basin or endorreic basin) is a drainage basin that normally retains water and allows no outflow to other external bodies of water, such as rivers or oceans, but converges instead into lakes or swamps, permanent or seasonal, that equilibrate through evaporation.
Evaporitic mudflat
Evaporitic mudflats are regions of laterally extensive strata com-posed of stacked, shoaling-upward, matrix-dominated saline beds (1–5 m thick). c.f. Saltern
Extremophile
A microorganism, especially an archaean, that lives in conditions of extreme temperature, acidity, alkalinity, or chemical concentration
Epilimnion
The upper layer of water in a stratified lake
Fermentation
Describes a series of anaerobic transforma-tion processes whereby organic matter is broken down into compounds of smaller size, which are more reduced or more oxidized and eventually more assimilatable by living matter. When fermentation leads to organic acids and a lowering of pH, it is called acidogenesis. The microorganisms responsible for this are called acidogens.
Ferrel Cell
In the Ferrel cell, air flows poleward and eastward near the surface and equatorward and westward at higher altitudes; this movement is the reverse of the airflow in the Hadley cell.
Gram-negative and Gram-positive
Are responses to the Gram staining technique whereby microorganisms are first stained with crystal violet, then treated with an iodine solution, decolourized with alcohol, and counterstained with safranine. Gram-positive bacteria retain the violet stain; Gram-negative bacteria do not.
Halocline
A halocline (from Greek hals or halos 'salt' and klinein 'to slope') is a subtype of chemocline caused by a strong, vertical salinity gradient within a body of water (lake or ocean).
Halophile
An organism that needs high salt concentrations for growth.
Halotolerant
Halotolerance is tolerance to ionic stress, or the ability of an organism to grow at salt concentrations higher than those required for growth. Halotolerant organisms are able to survive at high salt concentrations but do not necessarilty require these conditions for growth.
Heliothermal lake
These lakes are usually saline, meromictic lakes, which means that when they stratify, only the upper layer of the water will mix. The layers are separated by a halocline, with the mixolimnion remaining fairly fresh and the lower monimolimnion containing a higher salt concentration. When this stratification falls within the photic zone, unusual events happen. Sunlight that reaches the monimolimnion heats the water. This heat cannot escape because the density of the saline lower layer is not significantly affected by increasing temperatures. The result is a heat trap at and below the halocline, where temperatures can easily reach 50°C and higher
Heterotrophic bacteria
Heterotrophic bacteria are a type of bacteria that take the sugars they need to survive and reproduce from their environment, rather than making the sugars themselves from carbon and hydrogen.
Heterotrophs
Heterotrophs (literally “feeders on others”) use organic molecules syn-thesized outside their body as a source of energy and carbon (consum-ers, detritovores, decomposers). They are saprophytes, obtaining their nutrients from dead organic matter. Most chemotrophs are autotrophic, but some are heterotrophs (chemoheterotrophs), which use inorganic oxidation for energy but use organic matter for carbon as well as sup-plemental energy. Photosynthetic bacteria have the biochemistry for either anoxygenic photosynthesis (non O2-producing) or oxygenic pho-tosynthesis (O2-producing). Most photosynthetic bacteria are auto-trophs that fix CO2 (photoautotrophs), but some rely on organic matter for their carbon (photoheterotrophs). Adaptive prokaryotes switch their modes of metabolism depending on environmental conditions
Holomictic
Brine body with a uniform temperature and density from top to bottom, this allows mixing of upper and lower parts of the brine mass.
Homoacetogenesis
Homoacetogenesis is acetogenesis usinggaseous hydrogen and carbon dioxide
Hypersaline
Encompasses all waters more saline than seawater (mesohaline, penesaline and supersaline)
Hypertrophication
Describes the presence of excessive nutrients in a water body
Hypolimnion
The layer of water in a stratified lake that lies below the chemocline or thermocline, and is noncirculating.
Intertropical Convergence Zone (ITCZ)
The Intertropical Convergence Zone (ITCZ), known by sailors as the doldrums or the calms because of its monotonous, windless weather, is the area where the northeast and southeast trade winds converge. It encircles Earth near the thermal equator, though its specific position varies seasonally. When it lies near the geographic Equator, it is called the near-equatorial trough. Where the ITCZ is drawn into and merges with a monsoonal circulation, it is sometimes referred to as a monsoon trough, a usage more common in Australia and parts of Asia
Isoprenoids
Are a major class of nonsaponifiable lipids that occur in plants, animals, and bacteria and are characterized by chains of modular groups of five carbon atoms in which the typical pattern has four of the carbon atoms in a linear chain and a single carbon attached at the carbon one position removed from the end of the chain. The term isoprenoid is derived from the name of the five-carbon, doubly unsaturated branched hydrocar-bon isoprene, which could in principle be the simplest monomeric chemical precursor for this class of compounds. Isoprenoids are also known as terpenes. Terpenes are usually grouped according to the number of isoprene (C5H8) units in the molecule: monoterpenes (C10H16) contain two such units; sesquiterpenes (C15H24), three; diter-penes (C20H32), four; triterpenes (C30H48), six; and tetraterpenes (C40H64), eight. The carotenoid pig-ments are the best known tetraterpenes
Lithoautotrophs
Lithoautotrophs depend upon inorganic compounds as electron donors for energy production.
La Niña
La Niña is a coupled ocean-atmosphere phenomenon that is the colder counterpart of El Niño, as part of the broader El Niño–Southern Oscillation (ENSO) climate pattern.
Lunette
A type of crescent-shaped dune composed of pelleted clay, quartz or gypsum, blown up along the edges or forming a local eroded high in a lake basin, especially in dry areas of Australia.
Meromixis
The property (of a lake or brine seaway) by which water below a certain depth does not circulate during overturn owing to its high density (usually the result of a high salt concentration)
Mesophiles
Are organisms that grow best in moderate temperatures, neither too hot nor too cold, typically between 15 and 40 C
Methanogen
Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and generally belong to the domain of archaea.
Mixolimnion
The upper layer of a meromictic lake or brine seaway; its upper waters are mixed by the wind and evaporation
Monimolimnion
The lower, dense persistent water layer of a meromictic lake or brine seaway that does not mix with the waters above.
Oligomictic or oligotrophic
Describes stratified water masses that mix or homogenize for short irregular periods every few years.
Photoautotrophs
Use light as a source of energy and CO2 as a source of carbon. Term comes from auto-trophs (literally “self-feeders”), which describes organisms capable of producing organic com-pounds from simple inorganic compounds
Platform evaporites
Are the other major type of ancient marine-fed evaporite. They formed on con-tinental margins throughout much more of Phaner-ozoic time than basinwides. Salt fills are 10–50 m thick, mostly CaSO4 and typically interbedded with normal-restricted marine carbonates. Stacked platform sections characterised by this style of accumulation encompass time frames of 1–10 Myr and are largely tied to times in earth history when climate was in greenhouse mode and the associated eustacy favoured widespread epicontinental seaways subject to periodic restriction
Red waters and brines
The pink to purple colours that typify many hypersaline water bodies come mostly from concentrations of carotenoid pigments present in the cytoplasm of various halotolerant and halophilic microorganisms. Most haloarchaea are red due to a high content of C-50 carotenoids of the bacterioruberin series. Photosynthetic cyanobacteria and eukaryotes (e.g. unicellular green algae of the genus Dunaliella) contribute to the pigmentation of the hypersaline waters thanks to the presence of chlorophylls and C-40 carotenoids (mostly all-trans- and 9-cis-b-carotene). Chlorophylls absorb red and blue wavelengths much more strongly than they absorb green wavelengths, which is why chlorophyll-bearing cyanobacteria appear green (Fig. 2B). The carotenoids and phycobiliproteins, on the other hand, strongly absorb green wavelengths. Algae and microbes with large amounts of carotenoid appear yellow to brown (such as carotene-rich forms of Dunaliella sp.), those microbes with large amounts of phycocyanin appear blue, and those with large amounts of phycoerythrin appear red. Pigment levels can indicate the stratification of the microbial community in any photoresponsive biomass in a brine column. Red wavelengths (long wavelengths) are absorbed in the first few metres of a brine column or the uppermost millimetre or two of a microbial mat (where chlorophyll utilizers flourish). Blue and green wavelengths (shorter) reach deeper into the brine column or into the sediment.
Sabkha
Describes any marine or continental saltflat where a variety of efflorescent and displacive salts are accumulating at the surface and in the capillary zone, above a relatively shallow water table.
Saltern
Salterns are where extensive units of shallow-subaqueous evaporite beds (5–50 m thick) were deposited across hundreds of kilometres in the hypersaline portions of an ancient evaporite lake or seaway. Deposition took place in both marine-fed and continental settings. c.f. evaporitic mudflat.
Saprophytes
Obtain nourishment by absorbing dissolved organic material; especially from the products of organic breakdown and decay
Schizohaline
Describes waters subject to substantial ongoing salinity changes and periodically pass from brackish to hypersaline
Soda Lake
Soda lakes —have saline waters with sodium (Na) and carbonate species (HCO3 + CO3) as the dominant ions and typically exceed a pH of 9. Soda-lake waters also commonly have high concentrations of chloride, variable concentrations of sulphate and potassium, but they have very low concentrations of the alkaline earths.
Sulphur oxidising bacteria
Sulphur oxidising bacteria (SOB) are aerobic, anaerobic or facultative, and most of them are obligate or facultative autotrophs, that can either use carbon dioxide or organic compounds as a source of carbon (mixotrophs)
Sulphur reducing bacteria
Sulphur reducing bacteria (SRB) get their energy by reducing elemental sulfur to hydrogen sulfide. They couple this reaction with the oxidation of acetate, succinate or other organic compounds. Several types of bacteria and many non-methanogenic archaea can reduce sulfur.
Thermocline
The temperature border at which warmer and cooler waters meet in an ocean, sea, lake, or other body of water.
Third domain of life
In the late 1970s, Professor Carl Woese proposed, on the basis of ribosomal RNA affiliations (gene mapping), that life be divided into three domains instead of two, namely; Eukaryota, Eubacteria, and Archaebac-teria (Woese, 1993). He later decided that the term Archaebacteria was a misnomer, and shortened it to Archaea and Eubacteria to Bacteria. Since the 1970s, DNA base-pair studies (aka genomic stu-dies or gene sequencing) have shown that Archaea are as different from Bacteria as from Homo sapiens. This new approach to taxonomy is still working its way through the scientific community and some books and articles still ocassionally refer to archaea as types of bacteria. Prior to genomic studies, and based on their morphology and staining response, the archaeal Halobacteriaceae were grouped with the bacterial Gram-negative rods (a gram positive or gram negative description indicates whether or not the bacterial cell wall reacts with Gram’s stain).
Uniformitarianism
The doctrine suggesting that Earth's geologic processes acted in the same manner and with essentially the same intensity in the past as they do in the present and that such uniformity is sufficient to account for all geologic change.
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