Nitrification: A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.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.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.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.Nitrobacter: A genus of gram-negative, rod-shaped bacteria that oxidizes nitrites to nitrates. Its organisms occur in aerobic environments where organic matter is being mineralized, including soil, fresh water, and sea water.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)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.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.Brachiaria: A plant genus of the family POACEAE originating from the savanna of eastern Africa. It is widely grown for livestock forage.Bradyrhizobiaceae: A proposed family of bacteria belonging to the alpha-2 subgroup of PROTEOBACTERIA.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.Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.Nitrates: Inorganic or organic salts and esters of nitric acid. These compounds contain the NO3- radical.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.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.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.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.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.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.Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.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.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.Nitrogen Compounds: Inorganic compounds that contain nitrogen as an integral part of the molecule.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.Waste Disposal, Fluid: The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.Gram-Negative Chemolithotrophic Bacteria: A large group of bacteria including those which oxidize ammonia or nitrite, metabolize sulfur and sulfur compounds, or deposit iron and/or manganese oxides.Sewage: Refuse liquid or waste matter carried off by sewers.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).Waste Water: Contaminated water generated as a waste product of human activity.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.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.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)Genes, Archaeal: The functional genetic units of ARCHAEA.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.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.Nitrosomonadaceae: A family of gram-negative nitrifying bacteria, in the order Nitrosomonadales, class BETAPROTEOBACTERIA.Denaturing Gradient Gel Electrophoresis: Electrophoresis in which various denaturant gradients are used to induce nucleic acids to melt at various stages resulting in separation of molecules based on small sequence differences including SNPs. The denaturants used include heat, formamide, and urea.UzbekistanLife 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)Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.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.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)Picolines: A group of compounds that are monomethyl derivatives of pyridines. (From Dorland, 28th ed)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.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Trees: Woody, usually tall, perennial higher plants (Angiosperms, Gymnosperms, and some Pterophyta) having usually a main stem and numerous branches.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.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)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)Poaceae: A large family of narrow-leaved herbaceous grasses of the order Cyperales, subclass Commelinidae, class Liliopsida (monocotyledons). Food grains (EDIBLE GRAIN) come from members of this family. RHINITIS, ALLERGIC, SEASONAL can be induced by POLLEN of many of the grasses.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.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.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Oceans and Seas: A great expanse of continuous bodies of salt water which together cover more than 70 percent of the earth's surface. Seas may be partially or entirely enclosed by land, and are smaller than the five oceans (Atlantic, Pacific, Indian, Arctic, and Antarctic).Archaeal Proteins: Proteins found in any species of archaeon.Agriculture: The science, art or practice of cultivating soil, producing crops, and raising livestock.Tropical Climate: A climate which is typical of equatorial and tropical regions, i.e., one with continually high temperatures with considerable precipitation, at least during part of the year. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Alkynes: Hydrocarbons with at least one triple bond in the linear portion, of the general formula Cn-H2n-2.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)Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Sorghum: A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Water Pollutants, Chemical: Chemical compounds which pollute the water of rivers, streams, lakes, the sea, reservoirs, or other bodies of water.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.Biomass: Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop.Nitrate Reductase: An enzyme that catalyzes the oxidation of nitrite to nitrate. It is a cytochrome protein that contains IRON and MOLYBDENUM.Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.Sulfides: Chemical groups containing the covalent sulfur bonds -S-. The sulfur atom can be bound to inorganic or organic moieties.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Soil Pollutants: Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.Paracoccus denitrificans: A species of bacteria isolated from soil.Rivers: Large natural streams of FRESH WATER formed by converging tributaries and which empty into a body of water (lake or ocean).Plant Roots: The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)