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)Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Water Pollutants, Chemical: Chemical compounds which pollute the water of rivers, streams, lakes, the sea, reservoirs, or other bodies of water.Rivers: Large natural streams of FRESH WATER formed by converging tributaries and which empty into a body of water (lake or ocean).DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.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)Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.Deltaproteobacteria: A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.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.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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Estuaries: A partially enclosed body of water, and its surrounding coastal habitats, where saltwater from the ocean mixes with fresh water from rivers or streams. The resulting mixture of seawater and fresh water is called brackish water and its salinity can range from 0.5 to 35 ppt. (accessed http://oceanservice.noaa.gov/education/kits/estuaries/estuaries01_whatis.html)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).DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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)Lakes: Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.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.Water Pollution, Chemical: Adverse effect upon bodies of water (LAKES; RIVERS; seas; groundwater etc.) caused by CHEMICAL WATER POLLUTANTS.Pacific OceanRhizophoraceae: A plant family of the order Rhizophorales, subclass Rosidae, class Magnoliopsida, that includes mangrove trees.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.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)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.Water Pollutants: Substances or organisms which pollute the water or bodies of water. Use for water pollutants in general or those for which there is no specific heading.Wetlands: Environments or habitats at the interface between truly terrestrial ecosystems and truly aquatic systems making them different from each yet highly dependent on both. Adaptations to low soil oxygen characterize many wetland species.Uranium: Uranium. A radioactive element of the actinide series of metals. It has an atomic symbol U, atomic number 92, and atomic weight 238.03. U-235 is used as the fissionable fuel in nuclear weapons and as fuel in nuclear power reactors.Water Pollution: Contamination of bodies of water (such as LAKES; RIVERS; SEAS; and GROUNDWATER.)Environmental Monitoring: The monitoring of the level of toxins, chemical pollutants, microbial contaminants, or other harmful substances in the environment (soil, air, and water), workplace, or in the bodies of people and animals present in that environment.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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)Sulfates: Inorganic salts of sulfuric acid.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)Eutrophication: The enrichment of a terrestrial or aquatic ECOSYSTEM by the addition of nutrients, especially nitrogen and phosphorus, that results in a superabundant growth of plants, ALGAE, or other primary producers. It can be a natural process or result from human activity such as agriculture runoff or sewage pollution. In aquatic ecosystems, an increase in the algae population is termed an algal bloom.Bacteria, AnaerobicRNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Water Pollutants, Radioactive: Pollutants, present in water or bodies of water, which exhibit radioactivity.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Aroclors: Industrial chemicals which have become widespread environmental pollutants. Each aroclor is a mixture of chlorinated biphenyls (1200 series) or chlorinated terphenyls (5400 series) or a combination of both (4400 series).Soil Pollutants: Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.Water Movements: The flow of water in enviromental bodies of water such as rivers, oceans, water supplies, aquariums, etc. It includes currents, tides, and waves.Polycyclic Hydrocarbons, Aromatic: A major group of unsaturated cyclic hydrocarbons containing two or more rings. The vast number of compounds of this important group, derived chiefly from petroleum and coal tar, are rather highly reactive and chemically versatile. The name is due to the strong and not unpleasant odor characteristic of most substances of this nature. (From Hawley's Condensed Chemical Dictionary, 12th ed, p96)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).Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Petroleum: Naturally occurring complex liquid hydrocarbons which, after distillation, yield combustible fuels, petrochemicals, and lubricants.Groundwater: Liquid water present beneath the surface of the earth.Bays: An area of water mostly surrounded by land, usually smaller than a gulf, and affording access to the sea.Sulfides: Chemical groups containing the covalent sulfur bonds -S-. The sulfur atom can be bound to inorganic or organic moieties.Humic Substances: Organic matter in a state of advanced decay, after passing through the stages of COMPOST and PEAT and before becoming lignite (COAL). It is composed of a heterogenous mixture of compounds including phenolic radicals and acids that polymerize and are not easily separated nor analyzed. (E.A. Ghabbour & G. Davies, eds. Humic Substances, 2001).Marine Biology: The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.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.Paleontology: The study of early forms of life through fossil remains.Metals, Heavy: Metals with high specific gravity, typically larger than 5. They have complex spectra, form colored salts and double salts, have a low electrode potential, are mainly amphoteric, yield weak bases and weak acids, and are oxidizing or reducing agents (From Grant & Hackh's Chemical Dictionary, 5th ed)Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.Foraminifera: An order of amoeboid EUKARYOTES characterized by reticulating pseudopods and a complex life cycle with an alternation of generations. Most are less than 1mm in size and found in marine or brackish water.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.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)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)Thiotrichaceae: A family of colorless sulfur bacteria in the order Thiotrichales, class GAMMAPROTEOBACTERIA.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.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.HydrocarbonsChlorophenols: Phenols substituted with one or more chlorine atoms in any position.
Nankai 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.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.Bulloo-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.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.List of rivers of Brazil: This is a list of rivers in Brazil.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.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.Atmospheric methane: Atmospheric methane is the methane present in Earth's atmosphere. Atmospheric methane concentrations are of interest due to methane's impact on climate change, as it is one of the most potent greenhouse gases in Earth's atmosphere.BiodegradationDesulfococcus 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.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.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.Rogerstown Estuary: Rogerstown Estuary (Irish: Inbhear Bhaile Roiséir) is an estuary in Ireland. It is situated just north of the Donabate-Portrane peninsula, and also south of Rush, on Ireland's east coast about north of Dublin.Anoxic event: Oceanic anoxic events or anoxic events (anoxia conditions) refer to intervals in the Earth's past where portions of oceans become depleted in oxygen (O2) at depths over a large geographic area. During some of these events, euxinia develops - euxinia refers to anoxic waters that contain hydrogen sulfide.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).EcosystemSalt lake: Salt Lake (Disambiguation)}}Ecosystem of the North Pacific Subtropical Gyre: The North Pacific Subtropical Gyre (NPSG) is the largest contiguous ecosystem on earth. In oceanography, a subtropical gyre is a ring-like system of ocean currents rotating clockwise in the Northern Hemisphere and counterclockwise in the Southern Hemisphere caused by the Coriolis Effect.Kandelia obovata: Kandelia obovata (Traditional Chinese: 水筆仔、秋茄樹) is a species of plant in the Rhizophoraceae family, i.e.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.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.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).Coles PhillipsCalifornia coastal salt marsh: California's coastal salt marsh is a wetland plant community that occurs sporadically along the Pacific Coast from Humboldt Bay to San Diego. This salt marsh type is found in bays, harbors, inlets, and other protected areas subject to tidal flooding.Uranium mining debateUnited States regulation of point source water pollution: Point source water pollution comes from discrete conveyances and alters the chemical, biological, and physical characteristics of water. It is largely regulated by the Clean Water Act (CWA) of 1972.Index of geology articles: This is a list of all articles related to geology that cannot be readily placed on the following subtopic pages:Circumpolar Health Bibliographic DatabaseEutrophication: Eutrophication (Greek: eutrophia—healthy, adequate nutrition, development; ) or more precisely hypertrophication, is the ecosystem's response to the addition of artificial or natural nutrients, mainly phosphates, through detergents, fertilizers, or sewage, to an aquatic system.Schindler, David and Vallentyne, John R.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.Alkalimonas: Alkalimonas is a genus in the phylum Proteobacteria (Bacteria).PyromorphiteHydraulic action: Hydraulic action is erosion that occurs when the motion of water against a rock surface produces mechanical weathering. Most generally, it is the ability of moving water (flowing or waves) to dislodge and transport rock particles.Benzo(k)fluorantheneTable 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.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.Groundwater model: Groundwater models are computer models of groundwater flow systems, and are used by hydrogeologists. Groundwater models are used to simulate and predict aquifer conditions.Hudson Bay Mountain: Hudson Bay Mountain is an ultra prominent peak located above Smithers, British Columbia, Canada. It is the location of the Hudson Bay Mountain Resort (formerly Ski Smithers) ski resort.Sodium tetrasulfideHumic acid: Humic acid is a principal component of humic substances, which are the major organic constituents of soil (humus), peat and coal. It is also a major organic constituent of many upland streams, dystrophic lakes, and ocean water.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.Carbon–carbon bond: A carbon–carbon bond is a covalent bond between two carbon atoms. The most common form is the single bond: a bond composed of two electrons, one from each of the two atoms.Caninia (genus)Phytoextraction process: Phytoextraction is a subprocess of phytoremediation in which plants remove dangerous elements or compounds from soil or water, most usually heavy metals, metals that have a high density and may be toxic to organisms even at relatively low concentrations.http://www.Cibicides: Cibicides is a cosmopolitan genus of benthic foraminifera known from at least as far back as the Paleocene (Loeblich & Tappan, 1988) that extends down to the present.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.Heptadecanoic acidChaenocephalus 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.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 .Index of soil-related articles: This is an index of articles relating to soil.Unsaturated hydrocarbon: Unsaturated hydrocarbons are hydrocarbons that have double or triple covalent bonds between adjacent carbon atoms. Those with at least one carbon to carbon double bond are called alkenes and those with at least one carbon to carbon triple bond are called alkynes.Dichlorophenol
(1/2414) Desulfocella halophila gen. nov., sp. nov., a halophilic, fatty-acid-oxidizing, sulfate-reducing bacterium isolated from sediments of the Great Salt Lake.
A new halophilic sulfate-reducing bacterium, strain GSL-But2T, was isolated from surface sediment of the Southern arm of the Great Salt Lake, UT, USA. The organism grew with a number of straight-chain fatty acids (C4-C16), 2-methylbutyrate, L-alanine and pyruvate as electron donors. Butyrate was oxidized incompletely to acetate. Sulfate, but not sulfite or thiosulfate, served as an electron acceptor. Growth was observed between 2 and 19% (w/v) NaCl with an optimum at 4-5% (w/v) NaCl. The optimal temperature and pH for growth were around 34 degrees C and pH 6.5-7.3, respectively. The generation time under optimal conditions in defined medium was around 28 h, compared to 20 h in complex medium containing yeast extract. The G+C content was 35.0 mol%. 16S rRNA gene sequence analysis revealed that strain GSL-But2T belongs to the family Desulfobacteriaceae within the delta-subclass of the Proteobacteria and suggested that strain GSL-But2T represents a member of a new genus. The name Desulfocella halophila gen. nov., sp. nov. is proposed for this organism. The type strain of D. halophila is strain GSL-But2T (= DSM 11763T = ATCC 700426T). (+info)
(2/2414) Isolation from estuarine sediments of a Desulfovibrio strain which can grow on lactate coupled to the reductive dehalogenation of 2,4, 6-tribromophenol.
Strain TBP-1, an anaerobic bacterium capable of reductively dehalogenating 2,4,6-tribromophenol to phenol, was isolated from estuarine sediments of the Arthur Kill in the New York/New Jersey harbor. It is a gram-negative, motile, vibrio-shaped, obligate anaerobe which grows on lactate, pyruvate, hydrogen, and fumarate when provided sulfate as an electron acceptor. The organism accumulates acetate when grown on lactate and sulfate, contains desulfoviridin, and will not grow in the absence of NaCl. It will not utilize acetate, succinate, propionate, or butyrate for growth via sulfate reduction. When supplied with lactate as an electron donor, strain TBP-1 will utilize sulfate, sulfite, sulfur, and thiosulfate for growth but not nitrate, fumarate, or acrylate. This organism debrominates 2-, 4-, 2,4-, 2,6-, and 2,4,6-bromophenol but not 3- or 2,3-bromophenol or monobrominated benzoates. It will not dehalogenate monochlorinated, fluorinated, or iodinated phenols or chlorinated benzoates. Together with its physiological characteristics, its 16S rRNA gene sequence places it in the genus Desulfovibrio. The average growth yield of strain TBP-1 grown on a defined medium supplemented with lactate and 2,4,6-bromophenol is 3.71 mg of protein/mmol of phenol produced, and the yield was 1.42 mg of protein/mmol of phenol produced when 4-bromophenol was the electron acceptor. Average growth yields (milligrams of protein per millimole of electrons utilized) for Desulfovibrio sp. strain TBP-1 grown with 2,4,6-bromophenol, 4-bromophenol, or sulfate are 0.62, 0.71, and 1.07, respectively. Growth did not occur when either lactate or 2,4,6-bromophenol was omitted from the growth medium. These results indicate that Desulfovibrio sp. strain TBP-1 is capable of growth via halorespiration. (+info)
(3/2414) Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments.
Diversity of the nitrous oxide reductase (nosZ) gene was examined in sediments obtained from the Atlantic Ocean and Pacific Ocean continental shelves. Approximately 1,100 bp of the nosZ gene were amplified via PCR, using nosZ gene-specific primers. Thirty-seven unique copies of the nosZ gene from these marine environments were characterized, increasing the nosZ sequence database fourfold. The average DNA similarity for comparisons between all 49 variants of the nosZ gene was 64% +/- 10%. Alignment of the derived amino acid sequences confirmed the conservation of important structural motifs. A highly conserved region is proposed as the copper binding, catalytic site (CuZ) of the mature protein. Phylogenetic analysis demonstrated three major clusters of nosZ genes, with little overlap between environmental and culture-based groups. Finally, the two non-culture-based gene clusters generally corresponded to sampling location, implying that denitrifier communities may be restricted geographically. (+info)
(4/2414) Dense populations of a giant sulfur bacterium in Namibian shelf sediments.
A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA sequence data, these bacteria are closely related to the marine filamentous sulfur bacteria Thioploca, abundant in the upwelling area off Chile and Peru. Similar to Thioploca, the giant bacteria oxidize sulfide with nitrate that is accumulated to =800 millimolar in a central vacuole. (+info)
(5/2414) Environment and behavior of 2.5-million-year-old Bouri hominids.
The Hata Member of the Bouri Formation is defined for Pliocene sedimentary outcrops in the Middle Awash Valley, Ethiopia. The Hata Member is dated to 2.5 million years ago and has produced a new species of Australopithecus and hominid postcranial remains not currently assigned to species. Spatially associated zooarchaeological remains show that hominids acquired meat and marrow by 2.5 million years ago and that they are the near contemporary of Oldowan artifacts at nearby Gona. The combined evidence suggests that behavioral changes associated with lithic technology and enhanced carnivory may have been coincident with the emergence of the Homo clade from Australopithecus afarensis in eastern Africa. (+info)
(6/2414) Rhodococcus erythropolis DCL14 contains a novel degradation pathway for limonene.
Strain DCL14, which is able to grow on limonene as a sole source of carbon and energy, was isolated from a freshwater sediment sample. This organism was identified as a strain of Rhodococcus erythropolis by chemotaxonomic and genetic studies. R. erythropolis DCL14 also assimilated the terpenes limonene-1,2-epoxide, limonene-1,2-diol, carveol, carvone, and (-)-menthol, while perillyl alcohol was not utilized as a carbon and energy source. Induction tests with cells grown on limonene revealed that the oxygen consumption rates with limonene-1,2-epoxide, limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and carveol were high. Limonene-induced cells of R. erythropolis DCL14 contained the following four novel enzymatic activities involved in the limonene degradation pathway of this microorganism: a flavin adenine dinucleotide- and NADH-dependent limonene 1, 2-monooxygenase activity, a cofactor-independent limonene-1, 2-epoxide hydrolase activity, a dichlorophenolindophenol-dependent limonene-1,2-diol dehydrogenase activity, and an NADPH-dependent 1-hydroxy-2-oxolimonene 1,2-monooxygenase activity. Product accumulation studies showed that (1S,2S,4R)-limonene-1,2-diol, (1S, 4R)-1-hydroxy-2-oxolimonene, and (3R)-3-isopropenyl-6-oxoheptanoate were intermediates in the (4R)-limonene degradation pathway. The opposite enantiomers [(1R,2R,4S)-limonene-1,2-diol, (1R, 4S)-1-hydroxy-2-oxolimonene, and (3S)-3-isopropenyl-6-oxoheptanoate] were found in the (4S)-limonene degradation pathway, while accumulation of (1R,2S,4S)-limonene-1,2-diol from (4S)-limonene was also observed. These results show that R. erythropolis DCL14 metabolizes both enantiomers of limonene via a novel degradation pathway that starts with epoxidation at the 1,2 double bond forming limonene-1,2-epoxide. This epoxide is subsequently converted to limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and 7-hydroxy-4-isopropenyl-7-methyl-2-oxo-oxepanone. This lactone spontaneously rearranges to form 3-isopropenyl-6-oxoheptanoate. In the presence of coenzyme A and ATP this acid is converted further, and this finding, together with the high levels of isocitrate lyase activity in extracts of limonene-grown cells, suggests that further degradation takes place via the beta-oxidation pathway. (+info)
(7/2414) Role of methanogens and other bacteria in degradation of dimethyl sulfide and methanethiol in anoxic freshwater sediments.
The roles of several trophic groups of organisms (methanogens and sulfate- and nitrate-reducing bacteria) in the microbial degradation of methanethiol (MT) and dimethyl sulfide (DMS) were studied in freshwater sediments. The incubation of DMS- and MT-amended slurries revealed that methanogens are the dominant DMS and MT utilizers in sulfate-poor freshwater systems. In sediment slurries, which were depleted of sulfate, 75 micromol of DMS was stoichiometrically converted into 112 micromol of methane. The addition of methanol or MT to DMS-degrading slurries at concentrations similar to that of DMS reduced DMS degradation rates. This indicates that the methanogens in freshwater sediments, which degrade DMS, are also consumers of methanol and MT. To verify whether a competition between sulfate-reducing and methanogenic bacteria for DMS or MT takes place in sulfate-rich freshwater systems, the effects of sulfate and inhibitors, like bromoethanesulfonic acid, molybdate, and tungstate, on the degradation of MT and DMS were studied. The results for these sulfate-rich and sulfate-amended slurry incubations clearly demonstrated that besides methanogens, sulfate-reducing bacteria take part in MT and DMS degradation in freshwater sediments, provided that sulfate is available. The possible involvement of an interspecies hydrogen transfer in these processes is discussed. In general, our study provides evidence for methanogenesis as a major sink for MT and DMS in freshwater sediments. (+info)
(8/2414) Molecular analysis of microbial community structures in pristine and contaminated aquifers: field and laboratory microcosm experiments.
This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% beta- and gamma-Proteobacteria (B+G), 31 to 35% alpha-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems. (+info)