Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Ectothiorhodospiraceae: A family in the order Chromatiales, class GAMMAPROTEOBACTERIA. These are haloalkaliphilic, phototrophic bacteria that deposit elemental sulfur outside their cells.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.Chemoautotrophic Growth: Growth of organisms using AUTOTROPHIC PROCESSES for obtaining nutrients and chemotrophic processes for obtaining a primary energy supply. Chemotrophic processes are involved in deriving a primary energy supply from exogenous chemical sources. Chemotrophic autotrophs (chemoautotrophs) generally use inorganic chemicals as energy sources and as such are called chemolithoautotrophs. Most chemoautotrophs live in hostile environments, such as deep sea vents. They are mostly BACTERIA and ARCHAEA, and are the primary producers for those ecosystems.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Mediterranean SeaBetaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.North SeaBacteria: 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.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.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)Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Bacteriochlorophyll A: A specific bacteriochlorophyll that is similar in structure to chlorophyll a.Black Sea: An inland sea between Europe and Asia. It is connected with the Aegean Sea by the Bosporus, the Sea of Marmara, and the Dardanelles.Phosphoribosylaminoimidazolecarboxamide Formyltransferase: An enzyme that catalyzes the conversion of aminoimidazole-4-carboxamide ribonucleotide to 5-formyl-aminoimidazole-4-carboxamide ribonucleotide in the purine de novo synthesis pathway. It requires the cofactor N(10)-FORMYLTETRAHYDROFOLATE as the formyl donor.Alteromonadaceae: A family of marine, gram-negative PROTEOBACTERIA including the genera ALTEROMONAS; Colwellia; Idiomarina; MARINOBACTER; MORITELLA; PSEUDOALTEROMONAS; and SHEWANELLA.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.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.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.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Hydrothermal Vents: Hot springs on the ocean floor. They are commonly found near volcanically active places such as mid-oceanic ridges.Aquatic Organisms: Organisms that live in water.Xanthomonadaceae: A family of gram-negative bacteria, in the order Xanthomonadales, pathogenic to plants.Halomonas: A genus of gram-negative, rod-shaped or pleomorphic bacteria which are halotolerant. Members of this genus are capable of growth in sodium chloride concentrations of up to 20% or more. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Chromatiaceae: A family of phototrophic purple sulfur bacteria that deposit globules of elemental sulfur inside their cells. They are found in diverse aquatic environments.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.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)Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.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.Pacific OceanOceanospirillaceae: A family of gram-negative bacteria in the order Oceanospirillales.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.Plankton: Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Thiothrix: A genus of colorless, filamentous, rod-shaped bacteria in the family THIOTRICHACEAE, containing sulfur globules. Thiothrix species are found as components of BIOFILMS in irrigation systems and wastewater treatment plants, and in marine environments as endosymbionts.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Microbial Consortia: A group of different species of microorganisms that act together as a community.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.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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its 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).Hemiptera: A large order of insects characterized by having the mouth parts adapted to piercing or sucking. It is comprised of four suborders: HETEROPTERA, Auchenorrhyncha, Sternorrhyncha, and Coleorrhyncha.Quinones: Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Petroleum: Naturally occurring complex liquid hydrocarbons which, after distillation, yield combustible fuels, petrochemicals, and lubricants.Atlantic OceanPhototrophic Processes: Processes by which phototrophic organisms use sunlight as their primary energy source. Contrasts with chemotrophic processes which do not depend on light and function in deriving energy from exogenous chemical sources. Photoautotrophy (or photolithotrophy) is the ability to use sunlight as energy to fix inorganic nutrients to be used for other organic requirements. Photoautotrophs include all GREEN PLANTS; GREEN ALGAE; CYANOBACTERIA; and green and PURPLE SULFUR BACTERIA. Photoheterotrophs or photoorganotrophs require a supply of organic nutrients for their organic requirements but use sunlight as their primary energy source; examples include certain PURPLE NONSULFUR BACTERIA. 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.Epsilonproteobacteria: A group of proteobacteria consisting of chemoorganotrophs usually associated with the DIGESTIVE SYSTEM of humans and animals.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.Vibrionaceae: A family of gram-negative bacteria whose members predominate in the bacterial flora of PLANKTON; FISHES; and SEAWATER. Some members are important pathogens for humans and animals.Rhizosphere: The immediate physical zone surrounding plant roots that include the plant roots. It is an area of intense and complex biological activity involving plants, microorganisms, other soil organisms, and the soil.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.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.Leeching: The application of LEECHES to the body to draw blood for therapeutic purposes. Such medicinal leeching, an ancient medical practice, is still being used in microsurgery and the treatment of venous congestion or occlusion.Sodium Chloride: A ubiquitous sodium salt that is commonly used to season food.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.Shewanella: A genus of gram-negative, facultatively anaerobic rods. It is a saprophytic, marine organism which is often isolated from spoiling fish.Rivers: Large natural streams of FRESH WATER formed by converging tributaries and which empty into a body of water (lake or ocean).Bioelectric Energy Sources: Electric power supply devices which convert biological energy, such as chemical energy of metabolism or mechanical energy of periodic movements, into electrical energy.Heteroptera: A suborder of HEMIPTERA, called true bugs, characterized by the possession of two pairs of wings. It includes the medically important families CIMICIDAE and REDUVIIDAE. (From Dorland, 28th ed)Deltaproteobacteria: A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.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)Hot Springs: Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.Anthozoa: A class in the phylum CNIDARIA, comprised mostly of corals and anemones. All members occur only as polyps; the medusa stage is completely absent.Marinobacter: A genus of gram-negative, rod-shaped bacteria in the family ALTEROMONADACEAE. The inability to utilize carbohydrates is a distinguishing feature from other genera in the family.Metagenomics: The genomic analysis of assemblages of organisms.Arctic Regions: The Arctic Ocean and the lands in it and adjacent to it. It includes Point Barrow, Alaska, most of the Franklin District in Canada, two thirds of Greenland, Svalbard, Franz Josef Land, Lapland, Novaya Zemlya, and Northern Siberia. (Webster's New Geographical Dictionary, 1988, p66)Porifera: The phylum of sponges which are sessile, suspension-feeding, multicellular animals that utilize flagellated cells called choanocytes to circulate water. Most are hermaphroditic. They are probably an early evolutionary side branch that gave rise to no other group of animals. Except for about 150 freshwater species, sponges are marine animals. They are a source of ALKALOIDS; STEROLS; and other complex molecules useful in medicine and biological research.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Korea: Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.Phytoplankton: Free-floating minute organisms that are photosynthetic. The term is non-taxonomic and refers to a lifestyle (energy utilization and motility), rather than a particular type of organism. Most, but not all, are unicellular algae. Important groups include DIATOMS; DINOFLAGELLATES; CYANOBACTERIA; CHLOROPHYTA; HAPTOPHYTA; CRYPTOMONADS; and silicoflagellates.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.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)Soil Pollutants: Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.Nitrates: Inorganic or organic salts and esters of nitric acid. These compounds contain the NO3- radical.Bacterial Proteins: Proteins found in any species of bacterium.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).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)Gastrointestinal Tract: Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Genes, Bacterial: The functional hereditary units of BACTERIA.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).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.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Locomotion: Movement or the ability to move from one place or another. It can refer to humans, vertebrate or invertebrate animals, and microorganisms.Microscopy, Electron, Transmission: Electron microscopy in which the ELECTRONS or their reaction products that pass down through the specimen are imaged below the plane of the specimen.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: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.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)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.Genetic Variation: Genotypic differences observed among individuals in a population.