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.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Soil Pollutants: Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.Soil Pollutants, Radioactive: Pollutants, present in soil, which exhibit radioactivity.Trees: Woody, usually tall, perennial higher plants (Angiosperms, Gymnosperms, and some Pterophyta) having usually a main stem and numerous branches.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.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.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)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.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Agriculture: The science, art or practice of cultivating soil, producing crops, and raising livestock.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)Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.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.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)Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Fungi: A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.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.Environmental Remediation: Removal of ENVIRONMENTAL POLLUTANTS or contaminants for the general protection of the environment. This is accomplished by various chemical, biological, and bulk movement methods, in conjunction with ENVIRONMENTAL MONITORING.Desert Climate: A type of climate characterized by insufficient moisture to support appreciable plant life. It is a climate of extreme aridity, usually of extreme heat, and of negligible rainfall. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Metals, Heavy: Metals with high specific gravity, typically larger than 5. They have complex spectra, form colored salts and double salts, have a low electrode potential, are mainly amphoteric, yield weak bases and weak acids, and are oxidizing or reducing agents (From Grant & Hackh's Chemical Dictionary, 5th ed)Humic Substances: Organic matter in a state of advanced decay, after passing through the stages of COMPOST and PEAT and before becoming lignite (COAL). It is composed of a heterogenous mixture of compounds including phenolic radicals and acids that polymerize and are not easily separated nor analyzed. (E.A. Ghabbour & G. Davies, eds. Humic Substances, 2001).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.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.Crops, Agricultural: Cultivated plants or agricultural produce such as grain, vegetables, or fruit. (From American Heritage Dictionary, 1982)Nitrification: A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.Environmental Monitoring: The monitoring of the level of toxins, chemical pollutants, microbial contaminants, or other harmful substances in the environment (soil, air, and water), workplace, or in the bodies of people and animals present in that environment.Oligochaeta: A class of annelid worms with few setae per segment. It includes the earthworms such as Lumbricus and Eisenia.Water: A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Actinomycetales: An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.Agricultural Irrigation: The routing of water to open or closed areas where it is used for agricultural purposes.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.Carbon Cycle: The cycle by which the element carbon is exchanged between organic matter and the earth's physical environment.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)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.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.Environmental Pollution: Contamination of the air, bodies of water, or land with substances that are harmful to human health and the environment.Rain: Water particles that fall from the ATMOSPHERE.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)Pica: The persistent eating of nonnutritive substances for a period of at least one month. (DSM-IV)Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.2,4-Dichlorophenoxyacetic Acid: An herbicide with irritant effects on the eye and the gastrointestinal system.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.Nitrogen Compounds: Inorganic compounds that contain nitrogen as an integral part of the molecule.Petroleum: Naturally occurring complex liquid hydrocarbons which, after distillation, yield combustible fuels, petrochemicals, and lubricants.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Carbon Sequestration: Any of several processes for the permanent or long-term artificial or natural capture or removal and storage of carbon dioxide and other forms of carbon, through biological, chemical or physical processes, in a manner that prevents it from being released into the atmosphere.Herbicides: Pesticides used to destroy unwanted vegetation, especially various types of weeds, grasses (POACEAE), and woody plants. Some plants develop HERBICIDE RESISTANCE.Pseudomonas fluorescens: A species of nonpathogenic fluorescent bacteria found in feces, sewage, soil, and water, and which liquefy gelatin.Phosphorus: A non-metal element that has the atomic symbol P, atomic number 15, and atomic weight 31. It is an essential element that takes part in a broad variety of biochemical reactions.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Microbial Consortia: A group of different species of microorganisms that act together as a community.Colony Count, Microbial: Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.Actinobacteria: Class of BACTERIA with diverse morphological properties. Strains of Actinobacteria show greater than 80% 16S rDNA/rRNA sequence similarity among each other and also the presence of certain signature nucleotides. (Stackebrandt E. et al, Int. J. Syst. Bacteriol. (1997) 47:479-491)Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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.Organic Chemicals: A broad class of substances containing carbon and its derivatives. Many of these chemicals will frequently contain hydrogen with or without oxygen, nitrogen, sulfur, phosphorus, and other elements. They exist in either carbon chain or carbon ring form.China: A country spanning from central Asia to the Pacific Ocean.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.Aluminum Silicates: Any of the numerous types of clay which contain varying proportions of Al2O3 and SiO2. They are made synthetically by heating aluminum fluoride at 1000-2000 degrees C with silica and water vapor. (From Hawley's Condensed Chemical Dictionary, 11th ed)Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Plant Development: Processes orchestrated or driven by a plethora of genes, plant hormones, and inherent biological timing mechanisms facilitated by secondary molecules, which result in the systematic transformation of plants and plant parts, from one stage of maturity to another.Carbon Dioxide: A colorless, odorless gas that can be formed by the body and is necessary for the respiration cycle of plants and animals.
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