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Isotope analysis is the identification of isotopic signature, abundance of certain stable isotopes of chemical elements within organic and inorganic compounds. Isotopic analysis can be used to understand the flow of energy through a food web, to reconstruct past environmental and climatic conditions, to investigate human and animal diets, for food authentification, and a variety of other physical, geological, palaeontological and chemical processes. Stable isotope ratios are measured using mass spectrometry, which separates the different isotopes of an element on the basis of their mass-to-charge ratio.
A radioactive tracer, radiotracer, or radioactive label is a synthetic derivative of a natural compound in which one or more atoms have been replaced by a radionuclide. By virtue of its radioactive decay, it can be used to explore the mechanism of chemical reactions by tracing the path that the radioisotope follows from reactants to products. Radiolabeling or radiotracing is thus the radioactive form of isotopic labeling. In biological contexts, experiments that use radioisotope tracers are sometimes called radioisotope feeding experiments.
Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.
An arbuscular mycorrhiza (AM) is a type of mycorrhiza in which the symbiont fungus penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza .They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered.
In molecular biology, a hybridization probe(HP) is a fragment of DNA or RNA of usually 15–10000 nucleotide long which can be radioactively or fluorescently labeled. HP can be used to detect the presence of nucleotide sequences in analyzed RNA or DNA that are complementary to the sequence in the probe. The labeled probe is first denatured (by heating or under alkaline conditions such as exposure to sodium hydroxide) into single stranded DNA (ssDNA) and then hybridized to the target ssDNA (Southern blotting) or RNA (northern blotting) immobilized on a membrane or in situ.
Isotopic labeling is a technique used to track the passage of an isotope through chemical reaction, metabolic pathway, or a biological cell. The reactant is 'labeled' by replacing one or more specific atoms with their isotopes. The reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine the sequence the isotopic atom followed in the reaction or the cell's metabolic pathway. The nuclides used in isotopic labeling may be stable nuclides or radionuclides. In the latter case, the labeling is called radiolabeling.
Geobiology is a field of scientific research that explores the interactions between the physical Earth and the biosphere. It is a relatively young field, and its borders are fluid. There is considerable overlap with the fields of ecology, evolutionary biology, microbiology, paleontology, and particularly soil science and biogeochemistry. Geobiology applies the principles and methods of biology, geology, and soil science to the study of the ancient history of the co-evolution of life and Earth as well as the role of life in the modern world. Geobiologic studies tend to be focused on microorganisms, and on the role that life plays in altering the chemical and physical environment of the pedosphere, which exists at the intersection of the lithosphere, atmosphere, hydrosphere and/or cryosphere. It differs from biogeochemistry in that the focus is on processes and organisms over space and time rather than on global chemical cycles.
In chemistry, isotopologues are molecules that differ only in their isotopic composition. They have the same chemical formula and bonding arrangement of atoms, but at least one atom has a different number of neutrons than the parent.
An isotopic signature is a ratio of non-radiogenic 'stable isotopes', stable radiogenic isotopes, or unstable radioactive isotopes of particular elements in an investigated material. The ratios of isotopes in a sample material are measured by isotope-ratio mass spectrometry against an isotopic reference material. This process is called isotope analysis.
Oxygen isotope ratio cycles are cyclical variations in the ratio of the abundance of oxygen with an atomic mass of 18 to the abundance of oxygen with an atomic mass of 16 present in some substances, such as polar ice or calcite in ocean core samples, measured with the isotope fractionation. The ratio is linked to ancient ocean temperature which in turn reflects ancient climate. Cycles in the ratio mirror climate changes in the geological history of Earth.
Cholestane is a saturated tetracyclic triterpene. This 27-carbon biomarker is produced by diagenesis of cholesterol and is one of the most abundant biomarkers in the rock record. Presence of cholestane, its derivatives and related chemical compounds in environmental samples is commonly interpreted as an indicator of animal life and/or traces of O2, as animals are known for exclusively producing cholesterol, and thus has been used to draw evolutionary relationships between ancient organisms of unknown phylogenetic origin and modern metazoan taxa. Cholesterol is made in low abundance by other organisms (e.g., rhodophytes, land plants), but because these other organisms produce a variety of sterols it cannot be used as a conclusive indicator of any one taxon. It is often found in analysis of organic compounds in petroleum.
Stable Isotope Labeling by/with Amino acids in Cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitative proteomics.
Metabolic flux analysis (MFA) is an experimental fluxomics technique used to examine production and consumption rates of metabolites in a biological system. At an intracellular level, it allows for the quantification of metabolic fluxes, thereby elucidating the central metabolism of the cell. Various methods of MFA, including isotopically stationary metabolic flux analysis, isotopically non-stationary metabolic flux analysis, and thermodynamics-based metabolic flux analysis, can be coupled with stoichiometric models of metabolism and mass spectrometry methods with isotopic mass resolution to elucidate the transfer of moieties containing isotopic tracers from one metabolite into another and derive information about the metabolic network. Metabolic flux analysis (MFA) has many applications such as determining the limits on the ability of a biological system to produce a biochemical such as ethanol, predicting the response to gene knockout, and guiding the identification of bottleneck enzymes in metabolic networks for metabolic engineering efforts.
Phospholipid-derived fatty acids (PLFAs) are widely used in microbial ecology as chemotaxonomic markers of bacteria and other organisms. Phospholipids are the primary lipids composing cellular membranes. Phospholipids can be saponified, which releases the fatty acids contained in their diglyceride tail. Once the phospholipids of an unknown sample are saponified, the composition of the resulting PLFA can be compared to the PLFA of known organisms to determine the identity of the sample organism. PLFA analysis may be combined with other techniques, such as stable isotope probing to determine which microbes are metabolically active in a sample. PLFA analysis was pioneered by D.C. White at the University of Tennessee, in the early to mid 1980s.
The genus Methylophaga consists of halophilic methylotrophic members of the Gammaproteobacteria, all of which were isolated from marine or otherwise low water activity environments, such as the surface of marble or hypersaline lakes. The cells are rod-shaped. and are motile by a single polar flagellum.
Buoyant density centrifugation uses the concept of buoyancy to separate molecules in solution by their differences in density.
NanoSIMS is an analytical instrument manufactured by CAMECA which operates on the principle of secondary ion mass spectrometry. The NanoSIMS is used to acquire nanoscale resolution measurements of the elemental and isotopic composition of a sample. The NanoSIMS is able to create nanoscale maps of elemental or isotopic distribution, parallel acquisition of up to seven masses, isotopic identification, high mass resolution, subparts-per-million sensitivity with spatial resolution down to 50 nm.
Clumped isotopes are heavy isotopes that are bonded to other heavy isotopes. The relative abundance of clumped isotopes (and multiply-substituted isotopologues) in molecules such as methane, nitrous oxide, and carbonate is an area of active investigation. The carbonate clumped-isotope thermometer, or "13C–18O order/disorder carbonate thermometer", is a new approach for paleoclimate reconstruction, based on the temperature dependence of the clumping of 13C and 18O into bonds within the carbonate mineral lattice. This approach has the advantage that the 18O ratio in water is not necessary (different from the δ18O approach), but for precise paleotemperature estimation, it also needs very large and uncontaminated samples, long analytical runs, and extensive replication. Commonly used sample sources for paleoclimatological work include corals, otoliths, gastropods, tufa, bivalves, and foraminifera. Results are usually expressed as Δ47 (said as "cap 47"), which is the deviation of the ratio of isotopologues of CO2 with a molecular weight of 47 to those with a weight of 44 from the ratio expected if they were randomly distributed.
Methylophaga thiooxydans is a methylotrophic bacterium that requires high salt concentrations for growth. It was originally isolated from a culture of the algae Emiliania huxleyi, where it grows by breaking down dimethylsulfoniopropionate from E. hexleyi into dimethylsulfide and acrylate. M. thiooxydans has been implicated as a dominant organism in phytoplankton blooms, where it consumes dimethylsulfide, methanol and methyl bromide released by dying phytoplankton. It was also identified as one of the dominant organisms present in the plume following the Deepwater Horizon oil spill, and was identified as a major player in the breakdown of methanol in coastal surface water in the English channel.
Microbial oxidation of sulfur is the oxidation of sulfur by microorganisms to build their structural components. The oxidation of inorganic compounds is the strategy primarily used by chemolithotrophic microorganisms to obtain energy to survive, grow and reproduce. Some inorganic forms of reduced sulfur, mainly sulfide (H2S/HS−) and elemental sulfur (S0), can be oxidized by chemolithotrophic sulfur-oxidizing prokaryotes, usually coupled to the reduction of oxygen (O2) or nitrate (NO3−). Anaerobic sulfur oxidizers include photolithoautotrophs that obtain their energy from sunlight, hydrogen from sulfide, and carbon from carbon dioxide (CO2).
References
- ↑ Dumont MG, Murrell JC (June 2005). "Stable isotope probing - linking microbial identity to function". Nature Reviews. Microbiology. 3 (6): 499–504. doi:10.1038/nrmicro1162. PMID 15886694. S2CID 24051877.
- ↑ Neufeld JD, Dumont MG, Vohra J, Murrell JC (April 2007). "Methodological considerations for the use of stable isotope probing in microbial ecology". Microbial Ecology. 53 (3): 435–42. doi:10.1007/s00248-006-9125-x. PMID 17072677. S2CID 9417066.
- ↑ Radajewski S, Ineson P, Parekh NR, Murrell JC (February 2000). "Stable-isotope probing as a tool in microbial ecology". Nature. 403 (6770): 646–9. Bibcode:2000Natur.403..646R. doi:10.1038/35001054. PMID 10688198. S2CID 4395764.
- ↑ Schwartz E (February 2007). "Characterization of Growing Microorganisms in Soil by Stable Isotope Probing with H218O". Applied and Environmental Microbiology. 73 (8): 2541–2546. Bibcode:2007ApEnM..73.2541S. doi: 10.1128/AEM.02021-06 . PMC 1855593 . PMID 17322324. S2CID 18653420.
- ↑ Cupples AM, Shaffer EA, Chee-Sanford JC, Sims GK (2007). "DNA buoyant density shifts during 15N-DNA stable isotope probing". Microbiological Research. 162 (4): 328–34. doi:10.1016/j.micres.2006.01.016. PMID 16563712.
- ↑ Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa A.; Marks, Jane C.; Morrissey, Ember M. (2015). Schloss, P. D. (ed.). "Quantitative Microbial Ecology through Stable Isotope Probing". Applied and Environmental Microbiology. 81 (21): 7570–7581. Bibcode:2015ApEnM..81.7570H. doi:10.1128/AEM.02280-15. ISSN 0099-2240. PMC 4592864 . PMID 26296731.
- ↑ Starr, Evan P.; Shi, Shengjing; Blazewicz, Steven J.; Koch, Benjamin J.; Probst, Alexander J.; Hungate, Bruce A.; Pett-Ridge, Jennifer; Firestone, Mary K.; Banfield, Jillian F. (2021). "Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil". mSphere. 6 (5): e0008521. doi: 10.1128/msphere.00085-21 . PMC 8550312 . PMID 34468166. S2CID 237373088.
- ↑ Coskun, Ömer K.; Özen, Volkan; Wankel, Scott D.; Orsi, William D. (2019). "Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O". The ISME Journal. 13 (6): 1546–1559. doi:10.1038/s41396-019-0373-4. ISSN 1751-7370. PMC 6776007 . PMID 30783213.
- ↑ Hayer, Michaela; Schwartz, Egbert; Marks, Jane C.; Koch, Benjamin J.; Morrissey, Ember M.; Schuettenberg, Alexa A.; Hungate, Bruce A. (2016). "Identification of growing bacteria during litter decomposition in freshwater through quantitative stable isotope probing". Environmental Microbiology Reports. 8 (6): 975–982. doi: 10.1111/1758-2229.12475 . ISSN 1758-2229. PMID 27657357.