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.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.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.Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.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.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.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Epsilonproteobacteria: A group of proteobacteria consisting of chemoorganotrophs usually associated with the DIGESTIVE SYSTEM of humans and animals.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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)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.Fusobacteria: A phylum of anaerobic, gram-negative bacteria with a chemoorganotrophic heterotrophic metabolism. They are resident flora of the OROPHARYNX.Rhodobacter: A genus of gram-negative bacteria widely distributed in fresh water as well as marine and hypersaline habitats.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.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.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Bradyrhizobiaceae: A proposed family of bacteria belonging to the alpha-2 subgroup of PROTEOBACTERIA.Gram-Negative Facultatively Anaerobic Rods: A large group of facultatively anaerobic, rod-shaped bacteria that show up as pink (negative) when treated by the gram-staining method.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)Deltaproteobacteria: A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.Sulfonium Compounds: Sulfur compounds in which the sulfur atom is attached to three organic radicals and an electronegative element or radical.Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.Sewage: Refuse liquid or waste matter carried off by sewers.Cytophaga: A genus of gram-negative gliding bacteria found in SOIL; HUMUS; and FRESHWATER and marine habitats.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Bacteria, AerobicEcosystem: 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)Microbiota: The full collection of microbes (bacteria, fungi, virus, etc.) that naturally exist within a particular biological niche such as an organism, soil, a body of water, etc.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.Bacterial Proteins: Proteins found in any species of bacterium.Metagenomics: The genomic analysis of assemblages of organisms.Gram-Negative Bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.Gram-Negative Aerobic Bacteria: A large group of aerobic bacteria which show up as pink (negative) when treated by the gram-staining method. This is because the cell walls of gram-negative bacteria are low in peptidoglycan and thus have low affinity for violet stain and high affinity for the pink dye safranine.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genes, Bacterial: The functional hereditary units of BACTERIA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Gram-Negative Aerobic Rods and Cocci: A group of gram-negative bacteria consisting of rod- and coccus-shaped cells. They are both aerobic (able to grow under an air atmosphere) and microaerophilic (grow better in low concentrations of oxygen) under nitrogen-fixing conditions but, when supplied with a source of fixed nitrogen, they grow as aerobes.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.Gallionellaceae: A family of gram-negative bacteria in the order Nitrosomonadales, class BETAPROTEOBACTERIA. It contains a single genus Gallionella.Moritella: A genus of gram-negative, curved or straight rod-shaped bacteria, in the family ALTEROMONADACEAE. They are chemo-organotrophic, halophilic, and associated with cold marine habitats.Thiotrichaceae: A family of colorless sulfur bacteria in the order Thiotrichales, class GAMMAPROTEOBACTERIA.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.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.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.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).Pseudomonadaceae: A family of gram-negative bacteria usually found in soil or water and including many plant pathogens and a few animal pathogens.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)Acidobacteria: A physiologically diverse phylum of acidophilic, gram-negative bacteria found in a wide variety of habitats, but particularly abundant in soils and sediments.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.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Azoarcus: A genus of gram-negative, facultatively anaerobic bacteria including species which are often associated with grasses (POACEAE) and which fix nitrogen as well as species which anaerobically degrade toluene and other mono-aromatic hydrocarbons.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).Foot Rot: A disease of the horny parts and of the adjacent soft structures of the feet of cattle, swine, and sheep. It is usually caused by Corynebacterium pyogenes or Bacteroides nodosus (see DICHELOBACTER NODOSUS). It is also known as interdigital necrobacillosis. (From Black's Veterinary Dictionary, 18th ed)Waste Disposal, Fluid: The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.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.Caulobacter: A genus of gram-negative, aerobic, rod- or vibroid-shaped or fusiform bacteria that commonly produce a stalk. They are found in fresh water and soil and divide by binary transverse fission.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Sulfur-Reducing Bacteria: A group of gram-negative, anaerobic bacteria that is able to oxidize acetate completely to carbon dioxide using elemental sulfur as the electron acceptor.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.Waste Management: Disposal, processing, controlling, recycling, and reusing the solid, liquid, and gaseous wastes of plants, animals, humans, and other organisms. It includes control within a closed ecological system to maintain a habitable environment.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.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Marine Biology: The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.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).Dysbiosis: Changes in quantitative and qualitative composition of MICROBIOTA. The changes may lead to altered host microbial interaction or homeostatic imbalance that can contribute to a disease state often with inflammation.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.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.Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.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)Methylobacteriaceae: A family of gram-negative bacteria in the order Rhizobiales. Genera include METHYLOBACTERIUM, Protomonas, and Roseomonas.Thiobacillus: A genus of gram-negative, rod-shaped bacteria that derives energy from the oxidation of one or more reduced sulfur compounds. Many former species have been reclassified to other classes of PROTEOBACTERIA.Sulfur Compounds: Inorganic or organic compounds that contain sulfur as an integral part of the molecule.Bacteriochlorophylls: Pyrrole containing pigments found in photosynthetic bacteria.Petroleum: Naturally occurring complex liquid hydrocarbons which, after distillation, yield combustible fuels, petrochemicals, and lubricants.Burkholderia: A genus of gram-negative, aerobic, rod-shaped bacteria. Organisms in this genus had originally been classified as members of the PSEUDOMONAS genus but overwhelming biochemical and chemical findings indicated the need to separate them from other Pseudomonas species, and hence, this new genus was created.Microbial Consortia: A group of different species of microorganisms that act together as a community.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.Antarctic Regions: The continent lying around the South Pole and the southern waters of the Atlantic, Pacific, and Indian Oceans. It includes the Falkland Islands Dependencies. (From Webster's New Geographical Dictionary, 1988, p55)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)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.Acyl-Butyrolactones: Cyclic esters of acylated BUTYRIC ACID containing four carbons in the ring.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)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.Paracoccus: Gram-negative non-motile bacteria found in soil or brines.Flavobacterium: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in SOIL and WATER. Its organisms are also found in raw meats, MILK and other FOOD, hospital environments, and human clinical specimens. Some species are pathogenic in humans.Sphingomonadaceae: A family of gram-negative, asporogenous rods or ovoid cells, aerobic or facultative anaerobic chemoorganotrophs. They are commonly isolated from SOIL, activated sludge, or marine environments.Atlantic OceanGeological Phenomena: The inanimate matter of Earth, the structures and properties of this matter, and the processes that affect it.Bacteriochlorophyll A: A specific bacteriochlorophyll that is similar in structure to chlorophyll a.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)Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Pacific OceanArcobacter: A genus of gram-negative, aerotolerant, spiral-shaped bacteria isolated from water and associated with diarrhea in humans and animals.Genetic Variation: Genotypic differences observed among individuals in a population.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Gram-Positive Bacteria: Bacteria which retain the crystal violet stain when treated by Gram's method.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.Regulon: In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Bacteria, AnaerobicMediterranean SeaFungi: 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.Quorum Sensing: A phenomenon where microorganisms communicate and coordinate their behavior by the accumulation of signaling molecules. A reaction occurs when a substance accumulates to a sufficient concentration. This is most commonly seen in bacteria.Waste Water: Contaminated water generated as a waste product of human activity.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.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.Bartonella: A genus of gram-negative bacteria characteristically appearing in chains of several segmenting organisms. It occurs in man and arthropod vectors and is found only in the Andes region of South America. This genus is the etiologic agent of human bartonellosis. The genus Rochalimaea, once considered a separate genus, has recently been combined with the genus Bartonella as a result of high levels of relatedness in 16S rRNA sequence data and DNA hybridization data.Cyanobacteria: A phylum of oxygenic photosynthetic bacteria comprised of unicellular to multicellular bacteria possessing CHLOROPHYLL a and carrying out oxygenic PHOTOSYNTHESIS. Cyanobacteria are the only known organisms capable of fixing both CARBON DIOXIDE (in the presence of light) and NITROGEN. Cell morphology can include nitrogen-fixing heterocysts and/or resting cells called akinetes. Formerly called blue-green algae, cyanobacteria were traditionally treated as ALGAE.Methylococcaceae: A family of gram-negative, aerobic bacteria utilizing only one-carbon organic compounds and isolated from in soil and water.Neisseriaceae: A family of gram-negative, parasitic bacteria including several important pathogens of man.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.Rickettsiaceae: A family of small, gram-negative organisms, often parasitic in humans and other animals, causing diseases that may be transmitted by invertebrate vectors.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)Geology: The science of the earth and other celestial bodies and their history as recorded in the rocks. It includes the study of geologic processes of an area such as rock formations, weathering and erosion, and sedimentation. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Rhizobiaceae: A family of gram-negative bacteria which are saprophytes, symbionts, or plant pathogens.Alteromonas: A genus of gram-negative, straight or curved rods which are motile by means of a single, polar flagellum. Members of this genus are found in coastal waters and the open ocean. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Sulfides: Chemical groups containing the covalent sulfur bonds -S-. The sulfur atom can be bound to inorganic or organic moieties.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Bacteroides: A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.Thiosulfates: Inorganic salts of thiosulfuric acid possessing the general formula R2S2O3.Lakes: Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.Ice Cover: A thick mass of ICE formed over large regions of land; RIVERS; LAKES; ponds; or SEAWATER.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Gram-Negative Anaerobic Bacteria: A large group of anaerobic bacteria which show up as pink (negative) when treated by the Gram-staining method.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.Shewanella: A genus of gram-negative, facultatively anaerobic rods. It is a saprophytic, marine organism which is often isolated from spoiling fish.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Polychaeta: A class of marine annelids including sandworms, tube worms, clamworms, and fire worms. It includes also the genus Myxicola infundibulum.Agrobacterium tumefaciens: A species of gram-negative, aerobic bacteria isolated from soil and the stems, leafs, and roots of plants. Some biotypes are pathogenic and cause the formation of PLANT TUMORS in a wide variety of higher plants. The species is a major research tool in biotechnology.Soil Pollutants: Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.Sphingomonas: A genus of gram-negative, aerobic, rod-shaped bacteria characterized by an outer membrane that contains glycosphingolipids but lacks lipopolysaccharide. They have the ability to degrade a broad range of substituted aromatic compounds.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.Biofilms: Encrustations, formed from microbes (bacteria, algae, fungi, plankton, or protozoa) embedding in extracellular polymers, that adhere to surfaces such as teeth (DENTAL DEPOSITS); PROSTHESES AND IMPLANTS; and catheters. Biofilms are prevented from forming by treating surfaces with DENTIFRICES; DISINFECTANTS; ANTI-INFECTIVE AGENTS; and antifouling agents.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Periplasm: The space between the inner and outer membranes of a cell that is shared with the cell wall.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)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.Nitrate Reductase: An enzyme that catalyzes the oxidation of nitrite to nitrate. It is a cytochrome protein that contains IRON and MOLYBDENUM.4-Butyrolactone: One of the FURANS with a carbonyl thereby forming a cyclic lactone. It is an endogenous compound made from gamma-aminobutyrate and is the precursor of gamma-hydroxybutyrate. It is also used as a pharmacological agent and solvent.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.Nitrates: Inorganic or organic salts and esters of nitric acid. These compounds contain the NO3- radical.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.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Chloroflexi: Phylum of green nonsulfur bacteria including the family Chloroflexaceae, among others.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Wolinella: A genus of gram-negative, anaerobic, rod-shaped bacteria isolated from the bovine RUMEN, the human gingival sulcus, and dental PULPITIS infections.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Photosynthesis: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide using energy obtained from light rather than from the oxidation of chemical compounds. Photosynthesis comprises two separate processes: the light reactions and the dark reactions. In higher plants; GREEN ALGAE; and CYANOBACTERIA; NADPH and ATP formed by the light reactions drive the dark reactions which result in the fixation of carbon dioxide. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)Genes, Archaeal: The functional genetic units of ARCHAEA.Oxygenases: Oxidases that specifically introduce DIOXYGEN-derived oxygen atoms into a variety of organic molecules.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Biosynthetic Pathways: Sets of enzymatic reactions occurring in organisms and that form biochemicals by making new covalent bonds.Desulfovibrio: A genus of gram-negative, anaerobic, rod-shaped bacteria capable of reducing sulfur compounds to hydrogen sulfide. Organisms are isolated from anaerobic mud of fresh and salt water, animal intestines, manure, and feces.Campylobacter: A genus of bacteria found in the reproductive organs, intestinal tract, and oral cavity of animals and man. Some species are pathogenic.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.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.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Sulfates: Inorganic salts of sulfuric acid.Hydrocarbons

*  TIGR02420
Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function ... The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. ...
  http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR02420
*  Proteobacteria
... Click on an image to view larger version & data in a new window ... Proteobacteria. Version 10 March 2006 (temporary). http://tolweb.org/Proteobacteria/2302/2006.03.10 in The Tree of Life Web ...
  http://tolweb.org/Proteobacteria/2302/2006.03.10
*  Proteobacteria - Wikispecies
Proteobacteria Garrity et al., 2005. References[edit]. *Brenner, Krieg, Staley, and Garrity (ed.), 2005: Bergey's Manual of ... Proteobacteria in the World Register of Marine Species. Vernacular names[edit]. eesti: Proteobakterid. English: Purple Bacteria ... Phylum: Proteobacteria. Subphylum: Delta/epsilon subdivisions. Classes (overview): Acidithiobacillia - Alphaproteobacteria - ... 2, The Proteobacteria, Part C, Alpha-, Beta-, Delta-, and Epsilonproteobacteria. Springer, New York. ...
  https://species.wikimedia.org/wiki/Proteobacteria
*  Proteobacteria - Simple English Wikipedia, the free encyclopedia
Proteobacteria include a wide variety of pathogens, such as Escherichia coli, Salmonella, Vibrio, Helicobacter, and many other ... The Proteobacteria are a major phylum of bacteria.[1]. They are gram-negative bacteria. This means they do not retain the ... Proteobacteria: Purple bacteria and their relatives *alpha subdivision (purple non-sulfur bacteria, rhizobacteria, ... Retrieved from "https://simple.wikipedia.org/w/index.php?title=Proteobacteria&oldid=5776476" ...
  https://simple.wikipedia.org/wiki/Proteobacteria
*  The versatile epsilon-proteobacteria: key... & related info | Mendeley
The epsilon-proteobacteria have recently been recognized as globally ubiquitous in modern marine and terrestrial ecosystems, ... The epsilon-proteobacteria have recently been recognized as globally ubiquitous in modern marine and terrestrial ecosystems, ... and metabolic data in key sulphidic habitats and consider the ecological and geological potential of the epsilon-proteobacteria ...
  https://www.mendeley.com/research-papers/versatile-epsilonproteobacteria-key-players-sulphidic-habitats/
*  WoRMS - World Register of Marine Species - Proteobacteria
WoRMS (2005). Proteobacteria. In: Guiry, M.D. & Guiry, G.M. (2017). AlgaeBase. World-wide electronic publication, National ...
  http://www.marinespecies.org/aphia.php?p=taxdetails&id=178054&sortby=alpha
*  Bergey's Manual of Systematic Bacteriology: Volume Two: The Proteobacteria - Google Books
Volume 2 'The Proteobacteria.' (2004) Don J. Brenner, Noel R. Krieg, James T. Staley (Volume Editors), and George M. Garrity ( ... The volume provides descriptions of more than 2000 species in 538 genera that are assigned to the phylum Proteobacteria. This ... phototropic species of Bacteria belonging to the Proteobacteria and Firmicutes, which will be repeated in more detail in ... Bergey's Manual of Systematic Bacteriology: Volume Two: The Proteobacteria, Part 3. James T. Staley, Don J. Brenner, Noel R. ...
  https://books.google.co.in/books/about/Bergey_s_Manual_of_Systematic_Bacteriolo.html?id=dgejA4wa5R4C&hl=en
*  icd - Isocitrate dehydrogenase [NADP] - gamma proteobacterium HdN1 - icd gene & protein
gamma proteobacterium HdN1Imported. ,p>Information which has been imported from another database using automatic procedures.,/p ... tr,E1VK08,E1VK08_9GAMM Isocitrate dehydrogenase [NADP] OS=gamma proteobacterium HdN1 OX=83406 GN=icd PE=4 SV=1 ... cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › unclassified Gammaproteobacteria › unclassified ...
  http://www.uniprot.org/uniprot/E1VK08
*  Frontiers | Sulfur Metabolisms in Epsilon- and Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields | Microbiology
Epsilon-Proteobacteria use sulfur compounds for both electron-donors and -acceptors. On the other hand, gamma-Proteobacteria ... Epsilon-Proteobacteria use sulfur compounds for both electron-donors and -acceptors. On the other hand, gamma-Proteobacteria ... Many molecular ecological studies showed that chemoautotrophic epsilon- and gamma-Proteobacteria are predominant primary ... extending the energetically feasible habitats with versatile energy metabolisms in the epsilon-Proteobacteria and optimizing ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2011.00192/full
*  Proteobacteria - Wikipedia
Proteobacteria phyl. nov. In: Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2 (The Proteobacteria), part B (The ... Proteobacteria information from Palaeos. Proteobacteria. - J. P. Euzéby: List of Prokaryotic names with Standing in ... "Proteobacteria" distributed in the classes alpha, beta, gamma and epsilon. The best-studied "Proteobacteria" with respect to ... "Proteobacteria" is a major phylum of gram-negative bacteria. They include a wide variety of pathogens, such as Escherichia, ...
  https://en.wikipedia.org/wiki/Proteobacteria
*  Frontiers | Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center...
Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction ... including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes ... including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes ... gene sequences and the derived protein sequences from 152 type strains and 45 additional strains of phototrophic Proteobacteria ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2017.02679/full
*  Frontiers | Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling...
We focused on cbbM genes affiliated with the sulfur-oxidizing -proteobacteria cluster, whose members are known to dominate in ... We focused on cbbM genes affiliated with the sulfur-oxidizing -proteobacteria cluster, whose members are known to dominate in ... 2003) were not adequate for the amplification of the cbbM gene present in this group of γ-proteobacteria that thrive off the ... Keywords: RuBisCO, cbbM, γ-proteobacteria, OMZ, coastal-upwelling. Citation: Léniz B, Murillo AA, Ramírez-Flandes S and Ulloa O ...
  https://www.frontiersin.org/articles/10.3389/fmars.2017.00213/full
*  DIGITAL.CSIC: Rhodovarius lipocyclicus gen. nov. sp. nov., a new genus of the α-1 subclass of the Proteobacteria
The isolate also contained 18:1 2-OH and other fatty acids typical for members of the α-1 subclass of the Proteobacteria in ... nov., a new genus of the α-1 subclass of the Proteobacteria. ... a new genus of the α-1 subclass of the Proteobacteria for which ... the 16S rRNA gene sequence of the isolate indicated that it represents a new lineage in the α-1 subclass of the Proteobacteria ...
  https://digital.csic.es/handle/10261/102184
*  The Prokaryotes: A Handbook on the Biology of Bacteria: Volume 7: Proteobacteria: Delta and Epsilon Subclasses: Edited By: MM...
Proteobacteria: Delta and Epsilon Subclasses: NHBS - Edited By: MM Dworkin, S Falkow, E Rosenberg, K-H Schleifer and E ... The Prokaryotes: A Handbook on the Biology of Bacteria: Volume 7: Proteobacteria: Delta and Epsilon Subclasses. ... Proteobacteria. Delta Subclass. Epsilon Subclass.- Spirochaetes.- Chlorobiaceae.- Bacterioides and Cytophaga Group.- Chlamydia ...
  https://www.nhbs.com/the-prokaryotes-a-handbook-on-the-biology-of-bacteria-book
*  Proteobacteria | JAMS
Salicylate (SA) is a plant hormone and plays important roles in plant defence. SA is synthesized in the chloroplast and transmitted in the phloem. SA hydroxylase is a flavoprotein monooxygenase with the enzyme activity of degradation of SA and is a proximal component of the naphthalene degradation pathway in many bacteria. Candidatus Liberibacter asiaticus, the causal agent of the most devastating citrus disease, is phloem limited and encodes a SA hydroxylase. In this study, we have shown that the SA hydroxylase is functional in degrading SA and its analogs. Ca. L. asiaticus infected plants have reduced PR gene (PR1, PR2, and PR5) expression and SA accumulation in Duncan grapefruit and Valencia sweet orange in response to subsequent inoculation with Xanthomonas citri subsp. citri (Xac) Aw, which is nonpathogenic on both citrus varieties. Ca. L. asiaticus also increased citrus susceptibility to subsequent infection by X. citri. The bacterial populations of XacA and XacAw in grapefruit were ...
  http://jams.org.au/taxonomy/term/939
*  Small non-coding RNAs in the endosymbiotic diazotroph α-proteobacterium Sinorhizobium meliloti - Wikipedia
Batut J; Andersson SGE; O'Callaghan D (2004). "The evolution of chronic infection strategies in the α-proteobacteria". Nat Rev ... Sinorhizobium meliloti is an agronomically relevant α-proteobacterium able to induce the formation of new specialized organs, ... These findings anticipate a function for these sRNAs as trans-acting antisense riboregulators of α-proteobacteria-eukaryote ... The α-subdivision of the Proteobacteria includes Gram-negative microorganisms with diverse life styles; frequently involving ...
  https://en.wikipedia.org/wiki/Small_non-coding_RNAs_in_the_endosymbiotic_diazotroph_%CE%B1-proteobacterium_Sinorhizobium_meliloti
*  Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria |...
... which include different genera of the gamma-Proteobacteria and only one contains protein sequences from beta-Proteobacteria ( ... This, together with the fact that the HME2-RND genes from Cupriavidus and other Beta and Gamma-Proteobacteria are also found in ... In order to better understand the role of the RND efflux systems in the export of divalent cations in other Proteobacteria, we ... Characterization and distribution among proteobacteria. The CCNA_02805-02810 cluster is located at the end of a 60-kb genomic ...
  https://0-bmcmicrobiol-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1471-2180-13-79
*  Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome...
... granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich ... granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich ...
  http://sharptonlab.cgrb.oregonstate.edu/?q=node/24
*  The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like...
The γ-proteobacterium Nitrococcus mobilis was identified as sister of the Paulinella chromatophore and the PS-clade in the ... The γ-proteobacterium Nitrococcus mobilis represents the closest known relative to the donor of the carboxysomal operon. The ... The γ-proteobacterium Nitrococcus mobilis was identified as sister of the Paulinella chromatophore and the PS-clade in the ... The γ-proteobacterium Nitrococcus mobilis represents the closest known relative to the donor of the carboxysomal operon. The ...
  https://0-bmcevolbiol-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1471-2148-7-85
*  Study Identifies Bacteria Associated with Colorectal Cancer : Oncology Times
We found three particular groups-bacteroidetes, proteobacteria, and firmicutes-but we found that there was a higher abundance ... Compared with the controls, a significantly higher abundance of proteobacteria (12.9% vs 4.85%) and a lower abundance of ... Overall, firmicutes (62%), bacteroidetes (26%), and proteobacteria (11%) were the most dominant phyla. ... "Primarily, we found that there was a higher abundance of proteobacteria. ...
  http://journals.lww.com/oncology-times/Fulltext/2010/08100/Study_Identifies_Bacteria_Associated_with.10.aspx
*  9780077510589 - Connect Access Card with LearnSmart for | eCampus.com
The Proteobacteria 23. Firmicutes: The Low G ∙ C Gram-Positive Bacteria 24. A ctinobacteria: The High G ∙ C Gram-Positive ...
  http://www.ecampus.com/connectplus-access-card-learnsmart/bk/9780077510589
*  Gammaproteobacteria | definition of Gammaproteobacteria by Medical dictionary
proteobacteria. (redirected from Gammaproteobacteria). Also found in: Wikipedia. proteobacteria. (prō″tē-ō-băk-tē′rē-ă) A ... The phylum Proteobacteria presented 40% of Gammaproteobacteria species (100% of unclassified--three sequences) and 60% of ...
  http://medical-dictionary.thefreedictionary.com/Gammaproteobacteria
*  ereprof. dr. Paul De Vos
Introduction to the Proteobacteria Karel Kersters (UGent) , Paul De Vos (UGent) , Monique Gillis (UGent) , Jean Swings (UGent) ...
  https://biblio.ugent.be/person/801000355927?sort=year.desc&limit=10&start=230

Zetaproteobacteria: The class Zetaproteobacteria is the sixth and most recently described class of the Proteobacteria. Zetaproteobacteria can also refer to the group of organisms assigned to this class.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Exogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.Pelagibacter ubique: Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name, although it has not yet been validly published according to the bacteriological code.Alkalimonas: Alkalimonas is a genus in the phylum Proteobacteria (Bacteria).Candidatus Accumulibacter: Candidatus Accumulibacter is an unclassified group of Betaproteobacteria that currently contains only a single member, Candidatus Accumulibacter Phosphatis. C.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Coles PhillipsLung microbiome: The lung microbiota (or pulmonary microbial community) is a complex variety of microbes found in the lower respiratory tract particularly on the mucus layer and the epithelial surfaces (the lung microbiome refer to their genomes). These microbes include bacteria, yeasts, viruses and bacteriophages.Sulfurimonas: Sulfurimonas is a bacterial genus within the class Epsilonproteobacteria. The members of this group grow chemolithoautotrophically using zero valent sulfur, molecular hydrogen or reduced sulfur compounds as electron donors and nitrate, nitrite and oxygen as electron acceptors.Fecal coliform: A fecal coliform (British: faecal coliform) is a facultatively anaerobic, rod-shaped, gram-negative, non-sporulating bacterium. Coliform bacteria generally originate in the intestines of warm-blooded animals.Deep chlorophyll maximum: A deep chlorophyll maximum (DCM) is a subsurface maximum in the concentration of chlorophyll in the ocean or a lake. A DCM is not always present--sometimes there is more chlorophyll at the surface than at any greater depth--but it is a common feature of most aquatic ecosystems.Gemmatimonadetes: The Gemmatimonadetes are a family of bacteria, given their own phylum (Gemmatimonadetes). This bacterium makes up about 2% of soil bacterial communities and has been identified as one of the top nine phyla found in soils; yet, there are currently only six cultured isolates.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Adlercreutzia: Adlercreutzia is a genus in the phylum Actinobacteria (Bacteria).Creature House Expression: Creature House Expression was an award-winning vector graphics editor developed by Creature House in Hong Kong, founded by Alex S.C.Nitrosomonas europaea: Nitrosomonas europaea is a Gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite and lives in several places such as soil, sewage, freshwater, the walls of buildings and on the surface of monuments especially in polluted areas where the air contains high levels of nitrogen compounds.Domain (biology): In biological taxonomy, a domain (also superregnum, superkingdom, empire, or regio) is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese, an American microbiologist and biophysicist. According to the Woese system, introduced in 1990, the tree of life consists of three domains: Archaea (a term which Woese created), Bacteria, and Eukaryota.Alliance for Zero Extinction: Formed in 2000 and launched globally in 2005, the Alliance for Zero Extinction (AZE) comprises 100 non-governmental biodiversity conservation organizations working to prevent species extinctions by identifying and safeguarding sites where species evaluated to be Endangered or Critically Endangered under International Union for Conservation of Nature (IUCN) criteria only exist at one location on earth."Zero Extinction - Home.PropizepineNankai Trough gas hydrate site: Nankai Methane Hydrate Site (or Japanese Methane Hydrate R&D Program at Nankai, Nankai Trough Methane Hydrate Site) is located in the Nankai Trough, Japan.Desulfococcus oleovorans Strain Hxd3: Desulfococcus oleovorans Strain Hxd3 was isolated from the saline water phase of an oil-water separator from a northern German oil field.Aeckersberg, F.Suplatast tosilateAlkaliflexus: Alkaliflexus is a genus in the phylum Bacteroidetes (Bacteria).Angang Sewage Disposal Plant: The Angang Sewage Disposal Plant is a sewage treatment plant located in the city of Gyeongju, North Gyeongsang province, South Korea. It began operating in April, 2005 by the co-investment of the Government of North Gyeongsang and Gyeongju City with a fund of 44,300,000,000 won to install the facilities to prevent the pollution of Hyeongsan River which is a main water source for Gyeongju and Pohang residents.Cytophaga: Cytophaga is a genus of Gram-negative, gliding, rod-shaped bacteria.Pasteur point: The Pasteur point is a level of oxygen (about 0.3% by volume which is less than 1% of Present Atmospheric Level or PAL) above which aerobic microorganisms and facultative anaerobes adapt from fermentation to aerobic respiration.EcosystemBulloo-Bancannia drainage basin: The Bulloo-Bancannia drainage basin is a drainage basin that covers part of western Queensland and New South Wales. It is adjacent to the much larger Lake Eyre basin.BiodegradationFerric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Microbiota: A microbiota is "the ecological community of commensal, symbiotic and pathogenic microorganisms that literally share our body space". Joshua Lederberg coined the term, emphasising the importance of microorganisms inhabiting the human body in health and disease.Multidrug-resistant gram-negative bacteria: MDRGN bacteria is an abbreviation for multidrug resistant gram-negative bacteria. For hospitalized patients, and especially patients in intensive care units, these bacterial infections pose a serious and (as of 2010) rapidly emerging threat.Osiris TherapeuticsSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Global microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Continuous Plankton Recorder: The Continuous Plankton Recorder (CPR) survey is one of the longest running marine biological monitoring programmes in the world. Started in 1931 by Sir Alister Hardy, the CPR has provided marine scientists with their only measure of plankton communities on a pan-oceanic scale.Psychromonas antarctica: Psychromonas antarctica is a species of Proteobacteria. Ivanova (E.Thiomargarita namibiensis: Thiomargarita namibiensis is a gram-negative coccoid Proteobacterium, found in the ocean sediments of the continental shelf of Namibia. It is the largest bacteria ever discovered, as a rule in diameter, but sometimes attaining .Gijs Kuenen: Johannes Gijsbrecht Kuenen (born 9 December 1940, Heemstede) is a Dutch microbiologist who is professor emeritus at the Delft University of Technology and a visiting scientist at the University of Southern California. His research is influenced by, and a contribution to, the scientific tradition of the Delft School of Microbiology.Symbiosis Center of Health Care: Symbiosis Center of Health Care (SCHC) is an organization under Symbiosis Society which takes care of health of symbiosis family be it student or staff.http://www.Hydrogenothermaceae: The Hydrogenothermaceae family are bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, thermal ocean vents.Pseudomonadaceae: Pseudomonadaceae is a family of bacteria that includes the genera Azomonas, Azomonotrichon, Azorhizophilus, Azotobacter, Cellvibrio, Mesophilobacter, Pseudomonas (the type genus), Rhizobacter, Rugamonas, and Serpens.Skerman, McGowan and Sneath (editors): Approved Lists of Bacterial Names.Circumpolar Health Bibliographic DatabaseWhite Oil Pipeline: White Oil Pipeline is an oil pipeline extending from Port Qasim to the Pak-Arab Refinery (PARCO) at Qasba Gujrat, Multan District, Punjab, Pakistan.Pak-Arab Refinery's oil pipeline operationsRhizosphere: The rhizosphere is the narrow region of soil that is directly influenced by root secretions and associated soil microorganisms. Soil which is not part of the rhizosphere is known as bulk soil.Thermal cyclerBenzoyl-CoA 2,3-dioxygenase: Benzoyl-CoA 2,3-dioxygenase (, benzoyl-CoA dioxygenase/reductase, BoxBA, BoxA/BoxB system) is an enzyme with system name benzoyl-CoA,NADPH:oxygen oxidoreductase (2,3-hydroxylating). This enzyme catalyses the following chemical reactionHorizontal gene transfer in evolutionFoot rot: Foot rot, or infectious pododermatitis, is a hoof infection commonly found in sheep, goats, and cattle. As the name suggests, it rots away the foot of the animal, more specifically the area between the two toes of the affected animal.Deer Island Waste Water Treatment PlantBioreactorMolecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Sulfate-reducing bacteria: Sulfate-reducing bacteria are those bacteria and archaea that can obtain energy by oxidizing organic compounds or molecular hydrogen (H2) while reducing sulfate () to hydrogen sulfide (H2S). In a sense, these organisms "breathe" sulfate rather than oxygen in a form of anaerobic respiration.Diazotroph: Diazotrophs are bacteria and archaea that fix atmospheric nitrogen gas into a more usable form such as ammonia.Index of waste management articles: Articles related to waste management include:Bodega Marine Reserve: Bodega Marine Reserve is a nature reserve and marine reserve on the coast of northern California, located in the vicinity of the Bodega Marine Laboratory on Bodega Head. It is a unit of the University of California Natural Reserve System, that is administered by the University of California, Davis.Obligate aerobe: 300px|thumb|Aerobic and anaerobic [[bacteria can be identified by growing them in test tubes of thioglycollate broth: 1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.Table of standard reduction potentials for half-reactions important in biochemistry: The values below are standard reduction potentials for half-reactions measured at 25°C, 1 atmosphere and a pH of 7 in aqueous solution.Ammonia transporterGlucose-methanol-choline oxidoreductase family: In molecular biology, the glucose-methanol-choline oxidoreductase family (GMC oxidoreductase) is a family of enzymes with oxidoreductase activity.Rusticyanin: Rusticyanin is a copper-containing protein which is involved in electron-transfer, being a strong oxidant. It is a cupredoxin, or blue-copper protein due to its colour, and can be extracted from the bacteria Thiobacillus ferrooxidans.CapravirineBacteriochlorophyll: Bacteriochlorophylls are photosynthetic pigments that occur in various phototrophic bacteria. They were discovered by C.National Offshore Petroleum Safety Authority: The National Offshore Petroleum Safety Authority (NOPSA) was the occupational health and safety (OHS) regulator for the Australian offshore petroleum industry between 2005 and 2011. The role of regulator has been transferred to NOPSEMA - the National Offshore Petroleum Safety and Environmental Management Authority from the first of January 2012.Burkholderia kururiensis: Burkholderia kururiensis is a species of proteobacteria.Chaenocephalus aceratus: Chaenocephalus aceratus, the blackfin icefish, is a species of crocodile icefish known from around Bouvet Island and the northern Antarctic Peninsula where it occurs at depths of . This species grows to a length of TL.McIntosh and Filde's anaerobic jar: McIntosh and Filde's anaerobic jar is an instrument used in the production of an anaerobic environment. This method of anaerobiosis as others is used to culture bacteria which die or fail to grow in presence of oxygen (anaerobes).Eagle's minimal essential medium: Eagle's minimal essential medium (EMEM) is a cell culture medium developed by Harry Eagle that can be used to maintain cells in tissue culture.Quorum-quenching N-acyl-homoserine lactonase: Quorum-quenching N-acyl-homoserine lactonase (, acyl homoserine degrading enzyme, acyl-homoserine lactone acylase, AHL lactonase, AHL-degrading enzyme, AHL-inactivating enzyme, AHLase, AhlD, AhlK, AiiA, AiiA lactonase, AiiA-like protein, AiiB, AiiC, AttM, delactonase, lactonase-like enzyme, N-acyl homoserine lactonase, N-acyl homoserine lactone hydrolase, N-acyl-homoserine lactone lactonase, N-acyl-L-homoserine lactone hydrolase, quorum-quenching lactonase, quorum-quenching N-acyl homoserine lactone hydrolase) is an enzyme with system name N-acyl-L-homoserine-lactone lactonohydrolase.{{cite journal | title = The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase |author = Kim, M.Heptadecanoic acidFlavobacterium columnare: Flavobacterium columnare is a thin Gram-negative rod bacterium of the genus Flavobacterium. The name derives from the way in which the organism grows in rhizoid columnar formations.Sphingobium: Sphingobium species are different from other sphingomonads in that they are commonly isolated from soil; however, Sphingobium yanoikuyae was isolated from a clinical specimen. They can degrade a variety of chemicals in the environment such as aromatic and chloroaromatic compounds, phenols like nonylphenol and pentachlorophenol, herbicides such as (RS)-2-(4-chloro-2-methylphenoxy) propionic acid and hexachlorocyclohexane, and polycyclic aromatic hydrocarbons.In Memory of Celtic Frost: In Memory of... Celtic Frost is a Celtic Frost tribute album released in 1996.

(1/457) Marine bacterial isolates display diverse responses to UV-B radiation.

The molecular and biological consequences of UV-B radiation were investigated by studying five species of marine bacteria and one enteric bacterium. Laboratory cultures were exposed to an artificial UV-B source and subjected to various post-UV irradiation treatments. Significant differences in survival subsequent to UV-B radiation were observed among the isolates, as measured by culturable counts. UV-B-induced DNA photodamage was investigated by using a highly specific radioimmunoassay to measure cyclobutane pyrimidine dimers (CPDs). The CPDs determined following UV-B exposure were comparable for all of the organisms except Sphingomonas sp. strain RB2256, a facultatively oligotrophic ultramicrobacterium. This organism exhibited little DNA damage and a high level of UV-B resistance. Physiological conditioning by growth phase and starvation did not change the UV-B sensitivity of marine bacteria. The rates of photoreactivation following exposure to UV-B were investigated by using different light sources (UV-A and cool white light). The rates of photoreactivation were greatest during UV-A exposure, although diverse responses were observed. The differences in sensitivity to UV-B radiation between strains were reduced after photoreactivation. The survival and CPD data obtained for Vibrio natriegens when we used two UV-B exposure periods interrupted by a repair period (photoreactivation plus dark repair) suggested that photoadaptation could occur. Our results revealed that there are wide variations in marine bacteria in their responses to UV radiation and subsequent repair strategies, suggesting that UV-B radiation may affect the microbial community structure in surface water.  (+info)

(2/457) Identification of nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase.

Immunoblot analyses performed with three monoclonal antibodies (MAbs) that recognized the nitrite oxidoreductase (NOR) of the genus Nitrobacter were used for taxonomic investigations of nitrite oxidizers. We found that these MAbs were able to detect the nitrite-oxidizing systems (NOS) of the genera Nitrospira, Nitrococcus, and Nitrospina. The MAb designated Hyb 153-2, which recognized the alpha subunit of the NOR (alpha-NOR), was specific for species belonging to the genus Nitrobacter. In contrast, Hyb 153-3, which recognized the beta-NOR, reacted with nitrite oxidizers of the four genera. Hyb 153-1, which also recognized the beta-NOR, bound to members of the genera Nitrobacter and Nitrococcus. The molecular masses of the beta-NOR of the genus Nitrobacter and the beta subunit of the NOS (beta-NOS) of the genus Nitrococcus were identical (65 kDa). In contrast, the molecular masses of the beta-NOS of the genera Nitrospina and Nitrospira were different (48 and 46 kDa). When the genus-specific reactions of the MAbs were correlated with 16S rRNA sequences, they reflected the phylogenetic relationships among the nitrite oxidizers. The specific reactions of the MAbs allowed us to classify novel isolates and nitrite oxidizers in enrichment cultures at the genus level. In ecological studies the immunoblot analyses demonstrated that Nitrobacter or Nitrospira cells could be enriched from activated sludge by using various substrate concentrations. Fluorescence in situ hybridization and electron microscopic analyses confirmed these results. Permeated cells of pure cultures of members of the four genera were suitable for immunofluorescence labeling; these cells exhibited fluorescence signals that were consistent with the location of the NOS.  (+info)

(3/457) 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum.

Component D (HgdAB) of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum was purified to homogeneity. It is able to use component A from Acidaminococcus fermentans (HgdC) to initiate catalysis together with ATP, Mg2+ and a strong reducing agent such as Ti(III)citrate. Component D from C. symbiosum has a 6 x higher specific activity compared with that from A. fermentans and contains a second [4Fe-4S] cluster but the same amount of riboflavin 5'-phosphate (1.0 per heterodimeric enzyme, m = 100 kDa). Mossbauer spectroscopy revealed symmetric cube-type structures of the two [4Fe-4S]2+ clusters. EPR spectroscopy showed the resistance of the clusters to reducing agents, but detected a sharp signal at g = 2. 004 probably due to a stabilized flavin semiquinone. Three genes from C. symbiosum coding for components D (hgdA and hgdB) and A (hgdC) were cloned and sequenced. Primer extension experiments indicated that the genes are transcribed in the order hgdCAB from an operon only half the size of that from A. fermentans. Sequence comparisons detected a close relationship to the dehydratase system from A. fermentans and HgdA from Fusobacterium nucleatum, as well as to putative proteins of unknown function from Archaeoglobus fulgidus. Lower, but significant, identities were found with putative enzymes from several methanogenic Archaea and Escherichia coli, as well as with the mechanistically related benzoyl-CoA reductases from the Proteobacteria Rhodopseudomonas palustris and Thauera aromatica.  (+info)

(4/457) Simultaneous reduction of nitrate and selenate by cell suspensions of selenium-respiring bacteria.

Washed-cell suspensions of Sulfurospirillum barnesii reduced selenate [Se(VI)] when cells were cultured with nitrate, thiosulfate, arsenate, or fumarate as the electron acceptor. When the concentration of the electron donor was limiting, Se(VI) reduction in whole cells was approximately fourfold greater in Se(VI)-grown cells than was observed in nitrate-grown cells; correspondingly, nitrate reduction was approximately 11-fold higher in nitrate-grown cells than in Se(VI)-grown cells. However, a simultaneous reduction of nitrate and Se(VI) was observed in both cases. At nonlimiting electron donor concentrations, nitrate-grown cells suspended with equimolar nitrate and selenate achieved a complete reductive removal of nitrogen and selenium oxyanions, with the bulk of nitrate reduction preceding that of selenate reduction. Chloramphenicol did not inhibit these reductions. The Se(VI)-respiring haloalkaliphile Bacillus arsenicoselenatis gave similar results, but its Se(VI) reductase was not constitutive in nitrate-grown cells. No reduction of Se(VI) was noted for Bacillus selenitireducens, which respires selenite. The results of kinetic experiments with cell membrane preparations of S. barnesii suggest the presence of constitutive selenate and nitrate reduction, as well as an inducible, high-affinity nitrate reductase in nitrate-grown cells which also has a low affinity for selenate. The simultaneous reduction of micromolar Se(VI) in the presence of millimolar nitrate indicates that these organisms may have a functional use in bioremediating nitrate-rich, seleniferous agricultural wastewaters. Results with (75)Se-selenate tracer show that these organisms can lower ambient Se(VI) concentrations to levels in compliance with new regulations proposed for release of selenium oxyanions into the environment.  (+info)

(5/457) Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms.

The vertical distribution of sulfate-reducing bacteria (SRB) in aerobic wastewater biofilms grown on rotating disk reactors was investigated by fluorescent in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes. To correlate the vertical distribution of SRB populations with their activity, the microprofiles of O(2), H(2)S, NO(2)(-), NO(3)(-), NH(4)(+), and pH were measured with microelectrodes. In addition, a cross-evaluation of the FISH and microelectrode analyses was performed by comparing them with culture-based approaches and biogeochemical measurements. In situ hybridization revealed that a relatively high abundance of the probe SRB385-stained cells (approximately 10(9) to 10(10) cells per cm(3) of biofilm) were evenly distributed throughout the biofilm, even in the oxic surface. The probe SRB660-stained Desulfobulbus spp. were found to be numerically important members of SRB populations (approximately 10(8) to 10(9) cells per cm(3)). The result of microelectrode measurements showed that a high sulfate-reducing activity was found in a narrow anaerobic zone located about 150 to 300 microm below the biofilm surface and above which an intensive sulfide oxidation zone was found. The biogeochemical measurements showed that elemental sulfur (S(0)) was an important intermediate of the sulfide reoxidation in such thin wastewater biofilms (approximately 1,500 microm), which accounted for about 75% of the total S pool in the biofilm. The contribution of an internal Fe-sulfur cycle to the overall sulfur cycle in aerobic wastewater biofilms was insignificant (less than 1%) due to the relatively high sulfate reduction rate.  (+info)

(6/457) Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria.

Environmental contamination with compounds containing oxyanions of chlorine, such as perchlorate or chlorate [(per)chlorate] or chlorine dioxide, has been a constantly growing problem over the last 100 years. Although the fact that microbes reduce these compounds has been recognized for more than 50 years, only six organisms which can obtain energy for growth by this metabolic process have been described. As part of a study to investigate the diversity and ubiquity of microorganisms involved in the microbial reduction of (per)chlorate, we enumerated the (per)chlorate-reducing bacteria (ClRB) in very diverse environments, including pristine and hydrocarbon-contaminated soils, aquatic sediments, paper mill waste sludges, and farm animal waste lagoons. In all of the environments tested, the acetate-oxidizing ClRB represented a significant population, whose size ranged from 2.31 x 10(3) to 2.4 x 10(6) cells per g of sample. In addition, we isolated 13 ClRB from these environments. All of these organisms could grow anaerobically by coupling complete oxidation of acetate to reduction of (per)chlorate. Chloride was the sole end product of this reductive metabolism. All of the isolates could also use oxygen as a sole electron acceptor, and most, but not all, could use nitrate. The alternative electron donors included simple volatile fatty acids, such as propionate, butyrate, or valerate, as well as simple organic acids, such as lactate or pyruvate. Oxidized-minus-reduced difference spectra of washed whole-cell suspensions of the isolates had absorbance maxima close to 425, 525, and 550 nm, which are characteristic of type c cytochromes. In addition, washed cell suspensions of all of the ClRB isolates could dismutate chlorite, an intermediate in the reductive metabolism of (per)chlorate, into chloride and molecular oxygen. Chlorite dismutation was a result of the activity of a single enzyme which in pure form had a specific activity of approximately 1,928 micromol of chlorite per mg of protein per min. Analyses of the 16S ribosomal DNA sequences of the organisms indicated that they all belonged to the alpha, beta, or gamma subclass of the Proteobacteria. Several were closely related to members of previously described genera that are not recognized for the ability to reduce (per)chlorate, such as the genera Pseudomonas and Azospirllum. However, many were not closely related to any previously described organism and represented new genera within the Proteobacteria. The results of this study significantly increase the limited number of microbial isolates that are known to be capable of dissimilatory (per)chlorate reduction and demonstrate the hitherto unrecognized phylogenetic diversity and ubiquity of the microorganisms that exhibit this type of metabolism.  (+info)

(7/457) Geomicrobiology of subglacial ice above Lake Vostok, Antarctica.

Data from ice 3590 meters below Vostok Station indicate that the ice was accreted from liquid water associated with Lake Vostok. Microbes were observed at concentrations ranging from 2.8 x 10(3) to 3.6 x 10(4) cells per milliliter; no biological incorporation of selected organic substrates or bicarbonate was detected. Bacterial 16S ribosomal DNA genes revealed low diversity in the gene population. The phylotypes were closely related to extant members of the alpha- and beta-Proteobacteria and the Actinomycetes. Extrapolation of the data from accretion ice to Lake Vostok implies that Lake Vostok may support a microbial population, despite more than 10(6) years of isolation from the atmosphere.  (+info)

(8/457) Local sequence dependence of polyhydroxyalkanoic acid degradation in Hydrogenophaga pseudoflava.

The first order intracellular degradation of various polyhydroxyalkanoic acid (PHA) inclusions in Hydrogenophaga pseudoflava cells was investigated by analyzing the compositional and microstructural changes of the PHA using gas chromatography, (13)C NMR spectroscopy, and differential scanning calorimetry. Two types of PHA, copolymers and blend-type polymers, were separately accumulated in cells for comparison. The constituent monomers were 3-hydroxybutyric acid (3HB), 4-hydroxybutyric acid (4HB), and 3-hydroxyvaleric acid (3HV). It was found that the 3HB-4HB copolymer was degraded only when the polymer contained a minimal level of 3HB units. With the cells containing a 3HB/4HB blend-type polymer, only poly(3HB) was degraded, whereas poly(4HB) was not degraded, indicating the totally inactive nature of the intracellular depolymerase against poly(4HB). On the basis of the magnitude of the first order degradation rate constants, the relative substrate specificity of the depolymerase toward the constituting monomer units was determined to decrease in the order 3HB > 3HV > 4HB. (13)C NMR resonances of the tetrad, triad, and dyad sequences were analyzed for the samples isolated before and after degradation experiments. The results showed that the intracellular degradation depended on the local monomer sequence of the copolymers. The relative substrate specificity of the depolymerase determined from the NMR local sequence analysis agreed well with that obtained from the kinetics analysis. It is suggested that, without isolation and purification of the intracellular PHA depolymerase and "native" PHA substrates, the relative specificity of the enzyme as well as the microstructural heterogeneity of the PHA could be determined by measuring in situ the first order degradation rate constants of the PHA in cells.  (+info)



  • subclass
  • Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that it represents a new lineage in the α-1 subclass of the Proteobacteria, with the highest sequence similarity of 93.3% to the type strain of Muricoccus roseus. (csic.es)
  • The isolate also contained 18:1 2-OH and other fatty acids typical for members of the α-1 subclass of the Proteobacteria in addition to 10:0 2-OH in low amounts, not detected in members of closely related genera. (csic.es)
  • On the basis of the phylogenetic analyses, chemotaxonomic and biochemical characteristics, we propose that strain CCUG 44693T (CIP 108310T) represents a new genus of the α-1 subclass of the Proteobacteria for which we propose the name Rhodovarius lipocyclicus gen. nov. sp. (csic.es)
  • The Prokaryotes: "Vol. 6: Proteobacteria: Gamma Subclass. (wikipedia.org)
  • firmicutes
  • We found three particular groups-bacteroidetes, proteobacteria, and firmicutes-but we found that there was a higher abundance of proteobacteria in [colorectal cancer] cases than in controls," lead author Temitope O. Keku, PhD, of the Center for Gastrointestinal Biology and Disease at the University of North Carolina at Chapel Hill, said in a telephone interview. (lww.com)
  • Species
  • Sinorhizobium meliloti is an agronomically relevant α-proteobacterium able to induce the formation of new specialized organs, the so-called nodules, in the roots of its cognate legume hosts (i.e. some Medicago species). (wikipedia.org)
  • archaea
  • Three molecular forms of bona fide functional RuBisCO, named I, II and III, have been described to be directly involved in the CBB cycle, and are found in cyanobacteria, proteobacteria, some archaea, algae, and plants. (frontiersin.org)
  • genes
  • We focused on cbbM genes affiliated with the sulfur-oxidizing γ-proteobacteria cluster, whose members are known to dominate in oxygen-deficient marine environments and are highly abundant in the study area. (frontiersin.org)
  • include
  • Proteobacteria include a wide variety of pathogens , such as Escherichia coli , Salmonella , Vibrio , Helicobacter , and many other notable genera. (wikipedia.org)
  • higher
  • Compared with the controls, a significantly higher abundance of proteobacteria (12.9% vs 4.85%) and a lower abundance of bacteroidetes (29.14% vs 37.24%) were observed in those with an adenoma. (lww.com)