Denitrification: Nitrate reduction process generally mediated by anaerobic bacteria by which nitrogen available to plants is converted to a gaseous form and lost from the soil or water column. It is a part of the nitrogen cycle.Nitrous Oxide: Nitrogen oxide (N2O). A colorless, odorless gas that is used as an anesthetic and analgesic. High concentrations cause a narcotic effect and may replace oxygen, causing death by asphyxia. It is also used as a food aerosol in the preparation of whipping cream.Nitrite Reductases: A group of enzymes that oxidize diverse nitrogenous substances to yield nitrite. (Enzyme Nomenclature, 1992) EC 1.Nitrates: Inorganic or organic salts and esters of nitric acid. These compounds contain the NO3- radical.Nitrites: Salts of nitrous acid or compounds containing the group NO2-. The inorganic nitrites of the type MNO2 (where M=metal) are all insoluble, except the alkali nitrites. The organic nitrites may be isomeric, but not identical with the corresponding nitro compounds. (Grant & Hackh's Chemical Dictionary, 5th ed)Nitrification: A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.Nitrogen: An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.AcetylenePseudomonas stutzeri: A species of gram-negative bacteria in the genus PSEUDOMONAS, containing multiple genomovars. It is distinguishable from other pseudomonad species by its ability to use MALTOSE and STARCH as sole carbon and energy sources. It can degrade ENVIRONMENTAL POLLUTANTS and has been used as a model organism to study denitrification.Nitrate Reductase: An enzyme that catalyzes the oxidation of nitrite to nitrate. It is a cytochrome protein that contains IRON and MOLYBDENUM.Anaerobiosis: The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Nitrogen Isotopes: Stable nitrogen atoms that have the same atomic number as the element nitrogen, but differ in atomic weight. N-15 is a stable nitrogen isotope.Nitrogen Cycle: The circulation of nitrogen in nature, consisting of a cycle of biochemical reactions in which atmospheric nitrogen is compounded, dissolved in rain, and deposited in the soil, where it is assimilated and metabolized by bacteria and plants, eventually returning to the atmosphere by bacterial decomposition of organic matter.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Autotrophic Processes: The processes by which organisms use simple inorganic substances such as gaseous or dissolved carbon dioxide and inorganic nitrogen as nutrient sources. Contrasts with heterotrophic processes which make use of organic materials as the nutrient supply source. Autotrophs can be either chemoautotrophs (or chemolithotrophs), largely ARCHAEA and BACTERIA, which also use simple inorganic substances for their metabolic energy reguirements; or photoautotrophs (or photolithotrophs), such as PLANTS and CYANOBACTERIA, which derive their energy from light. Depending on environmental conditions some organisms can switch between different nutritional modes (autotrophy; HETEROTROPHY; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrient and energy requirements.Foraminifera: An order of amoeboid EUKARYOTES characterized by reticulating pseudopods and a complex life cycle with an alternation of generations. Most are less than 1mm in size and found in marine or brackish water.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.Oxidoreductases: The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)Nitrate Reductases: Oxidoreductases that are specific for the reduction of NITRATES.Ralstonia pickettii: The type species in the genus RALSTONIA. It is often found in the hospital ward as a contaminant of antiseptic and disinfectant solutions.Nitrogen Compounds: Inorganic compounds that contain nitrogen as an integral part of the molecule.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Paracoccus denitrificans: A species of bacteria isolated from soil.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Water Purification: Any of several processes in which undesirable impurities in water are removed or neutralized; for example, chlorination, filtration, primary treatment, ion exchange, and distillation. It includes treatment of WASTE WATER to provide potable and hygienic water in a controlled or closed environment as well as provision of public drinking water supplies.Nitrosomonas europaea: The type species of the genus NITROSOMONAS, a gram-negative chemolithotroph that oxidizes ammonia to nitrite. It is found in soil, sewage, freshwater, and on building walls, and especially in polluted areas where air contains high levels of nitrogen compounds.Bioreactors: Tools or devices for generating products using the synthetic or chemical conversion capacity of a biological system. They can be classical fermentors, cell culture perfusion systems, or enzyme bioreactors. For production of proteins or enzymes, recombinant microorganisms such as bacteria, mammalian cells, or insect or plant cells are usually chosen.Methylophilaceae: A family of gram-negative bacteria in the order Methylophilales.Alcaligenes faecalis: The type species of gram negative bacteria in the genus ALCALIGENES, found in soil. It is non-pathogenic, non-pigmented, and used for the production of amino acids.Biological Oxygen Demand Analysis: Testing for the amount of biodegradable organic material in a water sample by measuring the quantity of oxygen consumed by biodegradation of those materials over a specific time period.Acenaphthenes: Tricyclic ethylene-bridged naphthalene derivatives. They are found in petroleum residues and coal tar and used as dye intermediates, in the manufacture of plastics, and in insecticides and fungicides.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.Rhodocyclaceae: A family of gram-negative bacteria in the order Rhodocyclales, class BETAPROTEOBACTERIA. It includes many genera previously assigned to the family PSEUDOMONADACEAE.Sewage: Refuse liquid or waste matter carried off by sewers.Nitrogen Fixation: The process in certain BACTERIA; FUNGI; and CYANOBACTERIA converting free atmospheric NITROGEN to biologically usable forms of nitrogen, such as AMMONIA; NITRATES; and amino compounds.Ammonia: A colorless alkaline gas. It is formed in the body during decomposition of organic materials during a large number of metabolically important reactions. Note that the aqueous form of ammonia is referred to as AMMONIUM HYDROXIDE.Wetlands: Environments or habitats at the interface between truly terrestrial ecosystems and truly aquatic systems making them different from each yet highly dependent on both. Adaptations to low soil oxygen characterize many wetland species.Rivers: Large natural streams of FRESH WATER formed by converging tributaries and which empty into a body of water (lake or ocean).Quaternary Ammonium Compounds: Derivatives of ammonium compounds, NH4+ Y-, in which all four of the hydrogens bonded to nitrogen have been replaced with hydrocarbyl groups. These are distinguished from IMINES which are RN=CR2.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Ponds: Inland bodies of standing FRESHWATER usually smaller than LAKES. They can be man-made or natural but there is no universal agreement as to their exact size. Some consider a pond to be a small body of water that is shallow enough for sunlight to reach the bottom.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Ecosystem: A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)Waste Water: Contaminated water generated as a waste product of human activity.Achromobacter cycloclastes: A species of gram negative, aerobic, denitrifying bacteria in the genus ACHROMOBACTER.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Carbon: A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.Proteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Bradyrhizobium: A genus of gram-negative, aerobic, rod-shaped bacteria usually containing granules of poly-beta-hydroxybutyrate. They characteristically invade the root hairs of leguminous plants and act as intracellular symbionts.Waste Disposal, Fluid: The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Bacterial Proteins: Proteins found in any species of bacterium.Beggiatoa: A genus of colorless, filamentous bacteria in the family THIOTRICHACEAE whose cells contain inclusions of sulfur granules. When found in decaying seaweed beds and polluted water, its presence signals environmental degradation.Nitric Oxide: A free radical gas produced endogenously by a variety of mammalian cells, synthesized from ARGININE by NITRIC OXIDE SYNTHASE. Nitric oxide is one of the ENDOTHELIUM-DEPENDENT RELAXING FACTORS released by the vascular endothelium and mediates VASODILATION. It also inhibits platelet aggregation, induces disaggregation of aggregated platelets, and inhibits platelet adhesion to the vascular endothelium. Nitric oxide activates cytosolic GUANYLATE CYCLASE and thus elevates intracellular levels of CYCLIC GMP.Bacteria, AnaerobicOligochaeta: A class of annelid worms with few setae per segment. It includes the earthworms such as Lumbricus and Eisenia.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Life Support Systems: Systems that provide all or most of the items necessary for maintaining life and health. Provisions are made for the supplying of oxygen, food, water, temperature and pressure control, disposition of carbon dioxide and body waste. The milieu may be a spacecraft, a submarine, or the surface of the moon. In medical care, usually under hospital conditions, LIFE SUPPORT CARE is available. (From Webster's New Collegiate Dictionary)Genes, Bacterial: The functional hereditary units of BACTERIA.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Fertilizers: Substances or mixtures that are added to the soil to supply nutrients or to make available nutrients already present in the soil, in order to increase plant growth and productivity.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.Methanol: A colorless, flammable liquid used in the manufacture of FORMALDEHYDE and ACETIC ACID, in chemical synthesis, antifreeze, and as a solvent. Ingestion of methanol is toxic and may cause blindness.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Methane: The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)Ecological Systems, Closed: Systems that provide for the maintenance of life in an isolated living chamber through reutilization of the material available, in particular, by means of a cycle wherein exhaled carbon dioxide, urine, and other waste matter are converted chemically or by photosynthesis into oxygen, water, and food. (NASA Thesaurus, 1988)Baltic States: The collective name for the republics of ESTONIA; LATVIA; and LITHUANIA on the eastern shore of the Baltic Sea. (Webster's New Geographical Dictionary, 1988, p111)Rhizaria: A large supergroup of mostly amoeboid EUKARYOTES whose three main subgroups are CERCOZOA; FORAMINIFERA; and HAPLOSPORIDA. Nearly all of the species possess MITOCHONDRIA and historically many were considered ANIMALS.Oxygen: An element with atomic symbol O, atomic number 8, and atomic weight [15.99903; 15.99977]. It is the most abundant element on earth and essential for respiration.Fusarium: A mitosporic Hypocreales fungal genus, various species of which are important parasitic pathogens of plants and a variety of vertebrates. Teleomorphs include GIBBERELLA.Medical Waste Disposal: Management, removal, and elimination of biologic, infectious, pathologic, and dental waste. The concept includes blood, mucus, tissue removed at surgery or autopsy, soiled surgical dressings, and other materials requiring special control and handling. Disposal may take place where the waste is generated or elsewhere.Epsilonproteobacteria: A group of proteobacteria consisting of chemoorganotrophs usually associated with the DIGESTIVE SYSTEM of humans and animals.Alcaligenes: A genus of gram-negative, aerobic, motile bacteria that occur in water and soil. Some are common inhabitants of the intestinal tract of vertebrates. These bacteria occasionally cause opportunistic infections in humans.Piscirickettsiaceae: A family of gram-negative bacteria, in the order Thiotrichales.Heterotrophic Processes: The processes by which organisms utilize organic substances as their nutrient sources. Contrasts with AUTOTROPHIC PROCESSES which make use of simple inorganic substances as the nutrient supply source. Heterotrophs can be either chemoheterotrophs (or chemoorganotrophs) which also require organic substances such as glucose for their primary metabolic energy requirements, or photoheterotrophs (or photoorganotrophs) which derive their primary energy requirements from light. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; heterotrophy; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrients and energy requirements.Water Pollutants, Chemical: Chemical compounds which pollute the water of rivers, streams, lakes, the sea, reservoirs, or other bodies of water.Water Pollution, Chemical: Adverse effect upon bodies of water (LAKES; RIVERS; seas; groundwater etc.) caused by CHEMICAL WATER POLLUTANTS.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Dreissena: A genus of mussels in the family Dreissenidae, class BIVALVIA. They are found in both fresh and brackish water and are not native to North America. Accidentally introduced into the Great Lakes in 1986, they now proliferate widely throughout the United States.Achromobacter: A genus of gram-negative, strictly aerobic, non-spore forming rods. Soil and water are regarded as the natural habitat. They are sometimes isolated from a hospital environment and humans.Xanthomonadaceae: A family of gram-negative bacteria, in the order Xanthomonadales, pathogenic to plants.Manure: Accumulations of solid or liquid animal excreta usually from stables and barnyards with or without litter material. Its chief application is as a fertilizer. (From Webster's 3d ed)Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Burkholderiaceae: A family of gram negative, aerobic, non-sporeforming, rod-shaped bacteria.Azurin: A bacterial protein from Pseudomonas, Bordetella, or Alcaligenes which operates as an electron transfer unit associated with the cytochrome chain. The protein has a molecular weight of approximately 16,000, contains a single copper atom, is intensively blue, and has a fluorescence emission band centered at 308nm.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Pseudomonas aeruginosa: A species of gram-negative, aerobic, rod-shaped bacteria commonly isolated from clinical specimens (wound, burn, and urinary tract infections). It is also found widely distributed in soil and water. P. aeruginosa is a major agent of nosocomial infection.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Chromatography, Gas: Fractionation of a vaporized sample as a consequence of partition between a mobile gaseous phase and a stationary phase held in a column. Two types are gas-solid chromatography, where the fixed phase is a solid, and gas-liquid, in which the stationary phase is a nonvolatile liquid supported on an inert solid matrix.Nitrogen Oxides: Inorganic oxides that contain nitrogen.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Hydroxylamine: A colorless inorganic compound (HONH2) used in organic synthesis and as a reducing agent, due to its ability to donate nitric oxide.Paracoccus: Gram-negative non-motile bacteria found in soil or brines.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.Decapoda (Crustacea): The largest order of CRUSTACEA, comprising over 10,000 species. They are characterized by three pairs of thoracic appendages modified as maxillipeds, and five pairs of thoracic legs. The order includes the familiar shrimps, crayfish (ASTACOIDEA), true crabs (BRACHYURA), and lobsters (NEPHROPIDAE and PALINURIDAE), among others.Cells, Immobilized: Microbial, plant, or animal cells which are immobilized by attachment to solid structures, usually a column matrix. A common use of immobilized cells is in biotechnology for the bioconversion of a substrate to a particular product. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Nitrosomonas: A genus of gram-negative, ellipsoidal or rod-shaped bacteria whose major source of energy and reducing power is from the oxidation of ammonia to nitrite. Its species occur in soils, oceans, lakes, rivers, and sewage disposal systems.Methylococcus capsulatus: A species of METHYLOCOCCUS which forms capsules and is capable of autotrophic carbon dioxide fixation. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Greenhouse Effect: The effect of GLOBAL WARMING and the resulting increase in world temperatures. The predicted health effects of such long-term climatic change include increased incidence of respiratory, water-borne, and vector-borne diseases.Alkanes: The generic name for the group of aliphatic hydrocarbons Cn-H2n+2. They are denoted by the suffix -ane. (Grant & Hackh's Chemical Dictionary, 5th ed)Eutrophication: The enrichment of a terrestrial or aquatic ECOSYSTEM by the addition of nutrients, especially nitrogen and phosphorus, that results in a superabundant growth of plants, ALGAE, or other primary producers. It can be a natural process or result from human activity such as agriculture runoff or sewage pollution. In aquatic ecosystems, an increase in the algae population is termed an algal bloom.Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Atmosphere: The gaseous envelope surrounding a planet or similar body. (From Random House Unabridged Dictionary, 2d ed)Sulfur: An element that is a member of the chalcogen family. It has an atomic symbol S, atomic number 16, and atomic weight [32.059; 32.076]. It is found in the amino acids cysteine and methionine.Sulfides: Chemical groups containing the covalent sulfur bonds -S-. The sulfur atom can be bound to inorganic or organic moieties.
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