Biosynthetic control of the natural abundance of carbon 13 at specific positions within fatty acids in Escherichia coli. Evidence regarding the coupling of fatty acid and phospholipid synthesis

n-Alkane 13C/12C indicates differential metabolic controls of fatty lipid chain extension in C3 and C4 grasses

Fundamental differences in metabolic control of fatty acids chain extension are reflected in the contrasting carbon isotopic composition profiles of C3 and C4 grasses.

Fingerprinting eukaryotic metabolism across the animal kingdom using position-specific isotope analysis (PSIA) 13C/12C measurements

Despite differences in their overall metabolism, eukaryotes share a common mitochondrial biochemistry. We investigated how this fundamental biochemistry supports overall metabolism using a high-resolution carbon isotope approach, position-specific isotope analysis. We measured carbon isotope ¹³C/¹²C cycling in animals, focusing on amino acids that are formed in mitochondrial reactions and are most metabolically active. Carboxyl isotope determinations for amino acids showed strong signals related to common biochemical pathways. Contrasting isotope patterns were measured for metabolism associated with major life history patterns, including growth and reproduction. Turnover of proteins and lipids as well as gluoconeogensis dynamics could be estimated for these metabolic life histories. The high-resolution isotomics measurements fingerprinted metabolism and metabolic strategies across the eukaryotic animal kingdom, yielding results for humans, ungulates, whales, and diverse fish and invertebrates in a nearshore marine food web.

Using Stable Isotope Probing and Raman Microspectroscopy To Measure Growth Rates of Heterotrophic Bacteria

The suitability of stable isotope probing (SIP) and Raman microspectroscopy to measure growth rates of heterotrophic bacteria at the single-cell level was evaluated. Label assimilation into Escherichia coli biomass during growth on a complex ¹³C-labeled carbon source was monitored in time course experiments. ¹³C incorporation into various biomolecules was measured by spectral "red shifts" of Raman-scattered emissions. The ¹³C- and ¹²C-isotopologues of the amino acid phenylalanine (Phe) proved to be quantitatively accurate reporter molecules of cellular isotopic fractional abundances (f_cell). Values of f_cell determined by Raman microspectroscopy and independently by isotope ratio mass spectrometry (IRMS) over a range of isotopic enrichments were statistically indistinguishable. Progressive labeling of Phe in E. coli cells among a range of ¹³C/¹²C organic substrate admixtures occurred predictably through time. The relative isotopologue abundances of Phe determined by Raman spectral analysis enabled the accurate calculation of bacterial growth rates as confirmed independently by optical density (OD) measurements. The results demonstrate that combining SIP and Raman microspectroscopy can be a powerful tool for studying bacterial growth at the single-cell level on defined or complex organic ¹³C carbon sources, even in mixed microbial assemblages. IMPORTANCE Population growth dynamics and individual cell growth rates are the ultimate expressions of a microorganism's fitness under its environmental conditions, whether natural or engineered. Natural habitats and many industrial settings harbor complex microbial assemblages. Their heterogeneity in growth responses to existing and changing conditions is often difficult to grasp by standard methodologies. In this proof-of-concept study, we tested whether Raman microspectroscopy can reliably quantify the assimilation of isotopically labeled nutrients into E. coli cells and enable the determination of individual growth rates among heterotrophic bacteria. Raman-derived growth rate estimates were statistically indistinguishable from those derived by standard optical density measurements of the same cultures. Raman microspectroscopy can also be combined with methods for phylogenetic identification. We report the development of Raman-based techniques that enable researchers to directly link genetic identity to functional traits and rate measurements of single cells within mixed microbial assemblages, currently a major technical challenge in microbiological research.

Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system

RATIONALE

Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however.

METHODS

Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re-analyzing published data of different amino acids (AAs) in potato and in green alga.

RESULTS

Our re-analysis shows that biosynthesis pathways could be the reason for an apparently close-to-equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose-cultured green algae than in the autotrophic ones.

CONCLUSIONS

Application of the |Δα| matrix can help us to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets.

The isotopic structures of geological organic compounds

Organic compounds are ubiquitous in the Earth's surface, sediments and many rocks, and preserve records of geological, geochemical and biological history; they are also critical natural resources and major environmental pollutants. The naturally occurring stable isotopes of volatile elements (D, 13C, 15N, 17,18O, 33,34,36S) provide one way of studying the origin, evolution and migration of geological organic compounds. The study of bulk stable isotope compositions (i.e. averaged across all possible molecular isotopic forms) is well established and widely practised, but frequently results in non-unique interpretations. Increasingly, researchers are reading the organic isotopic record with greater depth and specificity by characterizing stable isotope ‘structures’ – the proportions of site-specific and multiply substituted isotopologues that contribute to the total rare-isotope inventory of each compound. Most of the technologies for measuring stable isotope structures of organic molecules have been only recently developed and to date have been applied only in an exploratory way. Nevertheless, recent advances have demonstrated that molecular isotopic structures provide distinctive records of biosynthetic origins, conditions and mechanisms of chemical transformation during burial, and forensic fingerprints of exceptional specificity. This paper provides a review of this young field, which is organized to follow the evolution of molecular isotopic structure from biosynthesis, through diagenesis, catagenesis and metamorphism.

Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging

Stable heavy isotopes co-exist with their lighter counterparts in all elements commonly found in biology. These heavy isotopes represent a low natural abundance in isotopic composition but impose great retardation effects in chemical reactions because of kinetic isotopic effects (KIEs). Previous isotope analyses have recorded pervasive enrichment or depletion of heavy isotopes in various organisms, strongly supporting the capability of biological systems to distinguish different isotopes. This capability has recently been found to lead to general decline of heavy isotopes in metabolites during yeast aging. Conversely, supplementing heavy isotopes in growth medium promotes longevity. Whether this observation prevails in other organisms is not known, but it potentially bears promise in promoting human longevity.

Biosynthesis of Membrane Lipids

The pathways in Escherichia coli and (largely by analogy) S. enterica remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of E. coli and S. enterica for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to E. coli introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.

Changes in δ(13)C of dark respired CO2 and organic matter of different organs during early ontogeny in peanut plants

Carbon isotope composition in respired CO2 and organic matter of individual organs were measured on peanut seedlings during early ontogeny in order to compare fractionation during heterotrophic growth and transition to autotrophy in a species with lipid seed reserves with earlier results obtained on beans. Despite a high lipid content in peanut seeds (48%) compared with bean seeds (1.5%), the isotope composition of leaf- and root-respired CO2 as well as its changes during ontogeny were similar to already published data on bean seedlings: leaf-respired CO2 became (13)C-enriched reaching -21.5‰, while root-respired CO2 became (13)C-depleted reaching around -31‰ at the four-leaf stage. The opposite respiratory fractionation in leaves vs. roots already reported for C3 herbs was thus confirmed for peanuts. However, contrarily to beans, the peanut cotyledon-respired CO2 was markedly (13)C-enriched, and its (13)C-depletion was noted from the two-leaf stage onwards only. Carbohydrate amounts being very low in peanut seeds, this cannot be attributed solely to their use as respiratory substrate. The potential role of isotope fractionation during glyoxylate cycle and/or gluconeogenesis on the (13)C-enriched cotyledon-respired CO2 is discussed.

Variation in bulk tissue, fatty acid and monosaccharide δ13C values between autotrophic and heterotrophic plant organs

The flowers of 23 species of grass and herb plants were collected from a mesotrophic grassland to assess natural variability in bulk, monosaccharide and fatty acid δ(13)C values from one plant community and were compared with previous analyses of leaves from the same species. The total mean bulk δ(13)C value of flower tissues was -28.1‰, and there was no significant difference between the mean δ(13)C(flower) values for grass (-27.8‰) and herb (-28.2‰) species. On average bulk δ(13)C(flower) values were 1.1‰ higher than bulk δ(13)C(leaf) values, however, the δ(13)C(flower) and δ(13)C(leaf) values of grasses did not differ between organs suggesting that carbon isotope discrimination is different in grass and herb species. The abundance of different monosaccharides abundance varied between plant types, i.e. xylose concentrations in the grass flowers were as high as 40%, compared with up to 15% in the herb species, but the general relationship δ(13)C(arabinose)>δ(13)C(xylose)>δ(13)C(glucose)>δ(13)C(galactose) which had been observed in leaves was similar in flowers (total mean δ(13)C values=-25.9‰, -27.2‰, -28.8‰ and -28.1‰, respectively). However, the average 5.4‰ depletion in the δ(13)C values of the C(16:0), C(18:2) and C(18:3) fatty acids in flowers compared to bulk tissue was significantly greater than observed for leaves. The trend C(16:0)<C(18:2)<C(18:3) previously observed in leaves was also observed in grass flowers (δ(13)C(C16:0)=-33.8‰; δ(13)C(C18:2)=-33.1‰; δ(13)C(C18:3)=-34.2‰) but not herb flowers (δ(13)C(C16:0)=-34.1‰; δ(13)C(C18:2)=-32.4‰; δ(13)C(C18:3)=-34.5‰). We conclude: (i) that the biological processes influencing carbon isotope discrimination in grass flowers are different from herbs flowers; and, (ii) that a range of post-photosynthetic fractionation effects caused the observed differences between flower and leaf δ(13)C values, especially the significant (13)C-depletion in flower fatty acid δ(13)C values.

Biosynthetic origin of the saw-toothed profile in delta(13)C and delta(2)H of n-alkanes and systematic isotopic differences between n-, iso- and anteiso-alkanes in leaf waxes of land plants

The n-fatty acids containing an even number of carbons (ECN-n-FAs) in higher plants are biosynthesised by repetitive addition of a two carbon unit from malonyl-ACP. The n-alkanes containing an odd number of carbon atoms (OCN-n-alkanes) are generally formed by the decarboxylation of ECN-n-FAs, but it is unknown how the less abundant even-carbon-numbered alkanes (ECN-n-alkanes) are biosynthesised in higher plants. There is a distinctive compositional pattern of incorporation of stable carbon ((13)C) and hydrogen ((2)H) isotopes in co-existing ECN- and OCN-n-alkanes in leaves of higher plants, such that the OCN n-alkanes are relatively enriched in (13)C but relatively depleted in (2)H against the ECN-n-alkanes. This is consistent with the OCN-n-fatty acids having a propionate precursor which is derived from reduction of pyruvate. A tentative pathway is presented with propionate produced by enzymatic reduction of pyruvate which is then thio-esterified with CoSH (coenzyme A thiol) in the chloroplast to form the terminal precursor molecule propionyl-CoA. This is then repetitively extended/elongated with the 2-carbon unit from malonyl-ACP to form the long chain OCN-n-fatty acids. The anteiso- and iso-alkanes in Nicotiana tabacum leaf waxes have previously been found to be systematically enriched in (13)C compared with the n-alkanes by Grice et al. (2008). This is consistent with the isotopic composition of their putative respective precursors (pyruvate as precursor for n-alkanes, valine for iso-alkanes and isoleucine for anteiso-alkanes). The current study complements that of Grice et al. (2008) and looks at the distribution of hydrogen isotopes. The n-alkanes were found to be more enriched in deuterium ((2)H) than the iso-alkanes which in turn were more enriched than the anteiso-alkanes. We propose therefore that the depletion of (2)H in the iso-alkanes, relative to the n-alkanes is the consequence of accepting highly (2)H-depleted hydrogen atoms from NADPH during their biosynthesis. The anteiso-alkanes are further depleted again because there are three NADPH-derived hydrogen atoms in their precursor isoleucine, as compared with only one NADPH-derived hydrogen in valine, the precursor of the iso-alkanes.

Methane oxidation in landfill cover soils, is a 10% default value reasonable?

We reviewed literature results from 42 determinations of the fraction of methane oxidized and 30 determinations of methane oxidation rate in a variety of soil types and landfill covers. Both column measurements and in situ field measurements were included. The means for the fraction of methane oxidized on transit across the soil covers ranged from 22 to 55% from clayey to sandy material. Mean values for oxidation rate ranged from 3.7 to 6.4 mol m(-2) d(-1) (52-102 g m(-2) d(-1)) for the different soil types. The overall mean fraction oxidized across all studies was 36% with a standard error of 6%. The overall mean oxidation rate across all studies was 4.5 mol m(-2) d(-1) +/- 1.0 (72 +/- 16 g m(-2)d(-1)). For the subset of 15 studies conducted over an annual cycle the fraction of methane oxidized ranged from 11 to 89% with a mean value of 35 +/- 6%, nearly identical to the overall mean. Nine of these studies were conducted in north Florida at 30 degrees N latitude and had a fraction oxidized of 27 +/- 4%. Five studies were conducted in northern Europe ( approximately 50-55 degrees N) and exhibited an average of 54 +/- 14%. One study, conducted in New Hampshire, had a value of 10%. The results indicate that the fraction of methane oxidized in landfill greater than the default value of 10%. Of the 42 determinations of methane oxidation reported, only four report values of 10% or less.

Interspecific variation in bulk tissue, fatty acid and monosaccharide delta(13)C values of leaves from a mesotrophic grassland plant community

The leaves of 37 grass, herb, shrub and tree species were collected from a mesotrophic grassland to assess natural variability in bulk, fatty acid and monosaccharide delta(13)C values of leaves from one plant community. The leaf tissue mean bulk delta(13)C value was -29.3 per thousand. No significant differences between tissue bulk delta(13)C values with life form were determined (P=0.40). On average, C(16:0), C(18:2) and C(18:3) constituted 89% of leaf tissue total fatty acids, whose delta(13)C values were depleted compared to whole leaf tissues. A general interspecific (between different species) trend for fatty acids delta(13)C values was observed, i.e. delta(13)C(16:0)<delta(13)C(18:2)<delta(13)C(18:3), although these values ranged widely between species, e.g. C(16:0) (-34.7 per thousand, Alisma plantago-aquatica; -44.0 per thousand, Leucanthemum vulgare), C(18:2) (-33.3 per thousand, Acer campestre; -44.2 per thousand, L. vulgare;) and C(18:3) (-34.3 per thousand, Bellis perennis; -41.8 per thousand, Plantago lanceolata). Average relative abundances of leaf monosaccharides arabinose, xylose, mannose, galactose and glucose were 12%, 13%, 5%, 12% and 54%, respectively. Mean delta(13)C values of these monosaccharides were -26.6 per thousand (arabinose), -27.2 per thousand (xylose), -30.9 per thousand (mannose), -30.0 per thousand (galactose) and -29.0 per thousand (glucose). The general relationship between individual monosaccharide delta(13)C values, delta(13)C(arabinose)>delta(13)C(xylose)>delta(13)C(glucose)>delta(13)C(galactose), was consistently observed. Therefore, we have shown (i) diversity in compound-specific delta(13)C values contributing to leaf bulk delta(13)C values; (ii) interspecific variability between bulk and compound-specific delta(13)C values of leaves of individual grassland species, and (iii) trends between individual fatty acid and monosaccharide delta(13)C values common to leaves of all species within one plant community.

Modelling of stable isotope fractionation by methane oxidation and diffusion in landfill cover soils

A technique to measure biological methane oxidation in landfill cover soils that is gaining increased interest is the measurement of stable isotope fractionation in the methane. Usually to quantify methane oxidation, only fractionation by oxidation is taken into account. Recently it was shown that neglecting the isotope fractionation by diffusion results in underestimation of the methane oxidation. In this study a simulation model was developed that describes gas transport and methane oxidation in landfill cover soils. The model distinguishes between 12CH4, 13CH4, and 12CH3D explicitly, and includes isotope fractionation by diffusion and oxidation. To evaluate the model, the simulations were compared with column experiments from previous studies. The predicted concentration profiles and isotopic profiles match the measured ones very well, with a root mean square deviation (RMSD) of 1.7 vol% in the concentration and a RMSD of 0.8 per thousand in the delta13C value, with delta13C the relative 13C abundance as compared to an international standard. Overall, the comparison shows that a model-based isotope approach for the determination of methane oxidation efficiencies is feasible and superior to existing isotope methods.

Tracing 2,4-D metabolism in Cupriavidus necator JMP134 with 13C-labelling technique and fatty acid profiling

The use of stable isotope probing of fatty acid methyl esters (FAME-SIP) is a powerful tool to study the microorganisms involved in xenobiotic biodegradation in soil. Nevertheless, it is important to determine how representative these molecules are of microorganisms both qualitatively and quantitatively. Using Cupriavidus necator JMP134 as a simple experimental model, we showed that the (13)C-labelling technique can be used both at a global (here defined as cellular, medium and CO(2)) and molecular level to study the metabolism of 2,4-Dichlorophenoxyacetic acid (2,4-D). Although isotopic fractionation among substrate, biomass and FAME were observed, this technique could be used when using a highly (13)C-labelled substrate. Global (13)C analyses gave similar results to those obtained with traditional (14)C-labelling methods. After 10 days of incubation 59% of ring-C was mineralized and about 30% remained in the liquid medium. A maximum of 11% was incorporated into the biomass after 3 days. The assimilation yield of chain-C into the biomass was about half that of ring-C, suggesting a preferential use of chain-C for energy acquisition. Molecular analysis of the lipid fraction evidenced that the incorporation of the labelled 2,4-D did not correspond to a bioaccumulation of pesticide residues but to the metabolism of the 2,4-D carbons for FAME synthesis. Provided the labelling is located on the benzenic ring, the assessment of (13)C-FAME is a robust method to quantify the incorporation of (13)C into the whole microbial biomass. However, the variability of the (13)C incorporation among FAME due to physiological processes has to be considered in complex biological systems. The coupling of bulk and molecular studies with a simple model as C. necator JMP134 is a good approach for testing FAME-SIP.

Methane oxidation in biofilters measured by mass-balance and stable isotope methods

Simultaneous flux and isotope measurements on compost and sand biofilters showed that the fraction of CH4 oxidized, calculated from delta13C measurements using a closed system model (f(oxir,C)), averaged only 0.455 of the fraction oxidized based on mass-balance measurements (f(oxm)). The discrepancy between f(oxm) and f(oxir,C) may be partly due to complete oxidation of a portion of the inflow gas, thereby eliminating its contribution to the emitted methane on which isotopic measurements are conducted. To relate f(oxir,C) and f(oxm) a simple binary closed-system model is proposed that assumes that f(oxir,C) refers to only part of the inflow, P, and that the remainder of inflow (1 - P) is completely oxidized before reaching the outlet. This model is compared to the standard open-system model. The H-isotope fraction oxidized (f(oxir,H)) was determined for a subset of samples and found to be not significantly different from f(oxir,C). The carbon isotope fractionation factor, alphaox,C = 1.0244, and the H-isotope fractionation factor, alphaox,H = 1.2370, were determined by incubation studies. Delta13C measurements indicated that the emitted flow was more strongly oxidized by the compost biofilters (f(oxir,C) = 0.362, f(oxm) = 0.757) than the sand biofilters (f(oxir,C) = 0.222, f(oxm) = 0.609).

Metabolic Routing of Dietary Nutrients in Birds: Effects of Diet Quality and Macronutrient Composition Revealed Using Stable Isotopes

During fall migration many songbirds switch from consuming primarily insects to consuming mostly fruit. Fruits with more carbohydrates and less protein may be sufficient to rebuild expended fat stores, but such fruits may be inadequate to replace catabolized protein. We manipulated the concentrations and isotopic signatures of macronutrients in diets fed to birds to study the effects of diet quality on metabolic routing of dietary nutrients. We estimated that approximately 45% and 75%, respectively, of the carbon in proteinaceous tissue of birds switched to high- or low-protein diets came from nonprotein dietary sources. In contrast, we estimated that approximately 100% and 20%-80%, respectively, of the nitrogen in proteinaceous tissues of birds switched to high- or low-protein diets was attributable to dietary protein. Thus, the routing and assimilation of dietary carbon and nitrogen differed depending on diet composition. As a result, delta (15)N of tissues collected from wild animals that consume high-quality diets may reliably indicate the dietary protein source, whereas delta (13)C of these same tissues is likely the product of metabolic routing of carbon from several macronutrients. These results have implications for how isotopic discrimination is best estimated and how we can study macronutrient routing in wild animals.

Hydrogen and carbon isotopic fractionations of lipid biosynthesis among terrestrial (C3, C4 and CAM) and aquatic plants

Compound-specific hydrogen and carbon isotopic compositions in n-alkanoic acids, phytol and sterols were determined for various plant classes (terrestrial C3-angiosperm; C3-gymnosperm; C4; crassulacean acid metabolism (CAM); and aquatic C3 plants) in order to investigate isotopic fractionations among various plant classes. In all plants, lipid biomolecules are depleted in both D (up to 324 per thousand ) and 13C (up to 14.7 per thousand ) relative to ambient water and bulk tissue, respectively. In addition, the magnitude of D- and 13C-depletion of lipid biomolecules is distinctive depending on plant classes. For example, C3 angiosperm n-alkanoic acids are less depleted in D (95+/-23 per thousand ) and 13C (4.3 +/- 2.5 per thousand ) relative to ambient water and bulk tissue, respectively, while C4 plant n-alkanoic acids are more depleted in D (119 +/- 15 per thousand ) and 13C (10.2 +/- 2.0 per thousand ). On the other hand, C3 angiosperm phytol and sterols are much more depleted in D (306 +/-12 per thousand for phytol, 211+/-15 per thousand for sterol) with less depletion in 13C (4.1 +/- 1.1 per thousand for phytol, 1.3 +/- 0.9 per thousand for sterol) relative to ambient water and bulk tissue, respectively, while C4 plant phytol and sterols are less depleted in D (254 +/- 7 per thousand for phytol, 186 +/- 13 per thousand for sterols) with much more depletion in 13C (9.0 +/- 1.2 per thousand for phytol, 5.0 +/- 1.1 per thousand for sterols). Among various plant classes, there is a positive correlation between the D- and 13C-depletion for n-alkanoic acids, while a negative correlation was found for phytol and sterols from the same plants.

Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

Rhizophora mangle L. (red mangrove) is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ) red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2-4 m and dwarf ~1-1.5 m). These height differences are coupled with very different stable carbon and nitrogen isotopic values[1] (mean tall δ ¹³C = -28.3‰, δ ¹⁵N = 0‰; mean tall δ ¹³C = -25.3‰, δ ¹⁵N = -10‰). To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ ¹³C and δ ¹⁵N) composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds) in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ ¹³C and δ ¹⁵N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ ¹³C and δ ¹⁵N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ ¹⁵N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in mangrove paleoecosystems.

Natural intramolecular isotope measurements in physiology: elements of the case for an effort toward high-precision position-specific isotope analysis

Chemical information available in organisms can be categorized into three major domains, macromolecular, small molecules, and isotope ratios. Information about physiological state is commonly obtained by qualitative and quantitative analysis in the macromolecular and small molecule domains. Genomics and proteomics are emerging approaches to analysis of macromolecules, and both areas yield definitive information on present physiological state. There is relatively little record of past physiological states of the individual available in these domains. Natural isotopic variability, particularly on an intramolecular level, is likely to retain more physiological history. Because of ubiquitous isotopic fractionation, every stereochemically unique position in every molecule has an isotope ratio that reflects the processes of synthesis and degradation. This fact highlights a vast amount of organismal chemical information that is essentially unstudied. Isotope measurements can be classified according to the chemical complexity of the analyte into bulk, compound-specific, and position-specific or intramolecular levels. Recent advances in analysis of isotope ratios are transforming natural science, and particularly answering questions about ecosystems using bulk methods; however, they have had relatively little impact on physiology. This may be because the vast complexities of physiological questions demand very selective information available in position-specific isotope analysis (PSIA). The relatively few high-precision PSIA studies, based on isotope ratio mass spectrometry (IRMS), have revealed intramolecular isotope ratio differences in pivotal physiological compounds including amino acids, glucose, glycerol, acetate, fatty acids, and purines. The majority of these analyses have been accomplished by laborious offline methods; however, recent advances in instrumentation presage rapid PSIA that will be necessary to attack real physiological problems. Gas-phase pyrolysis has been shown to be an effective method to determine (13)C/(12)C at high precision for molecular fragments, and technologies to extend C-based PSIA to N and other organic elements are emerging. Two related efforts are warranted, (a) development of rapid, convenient, and sensitive methods for high-precision PSIA, a necessary precursor to (b) a concerted investigation into the relationship of metabolic state to intramolecular isotope ratio. Inherent in this latter goal is the need to identify long-lived molecules in long-lived cells that retain a record of early isotopic conditions, as has been shown for post-mortem human neuronal DNA. Using known metabolic precursor-product relationships between intramolecular positions, future studies of physiological isotope fractionation should reveal the relationship of diet and environment to observed isotope ratio. This science of isotope physiology, or simply isotopics, should add an important tool for elucidation of early factors that effect later health, probably the most difficult class of biomedical issues.

Compound-specific isotope analysis. Application to archaeology, biomedical sciences, biosynthesis, environment, extraterrestrial chemistry, food science, forensic science, humic substances, microbiology, organic geochemistry, soil science and sport

The isotopic composition, for example, (14)C/(12)C, (13)C/(12)C, (2)H/(1)H, (15)N/(14)N and (18)O/(16)O, of the elements of matter is heterogeneous. It is ruled by physical, chemical and biological mechanisms. Isotopes can be employed to follow the fate of mineral and organic compounds during biogeochemical transformations. The determination of the isotopic composition of organic substances occurring at trace level in very complex mixtures such as sediments, soils and blood, has been made possible during the last 20 years due to the rapid development of molecular level isotopic techniques. After a brief glance at pioneering studies revealing isotopic breakthroughs at the molecular and intramolecular levels, this paper reviews selected applications of compound-specific isotope analysis in various scientific fields.

Natural abundance variations in stable isotopes and their potential uses in animal physiological ecology

Chemical, biological, and physical processes lead to distinctive "isotopic signatures" in biological materials that allow tracing of the origins of organic substances. Isotopic variation has been extensively used by plant physiological ecologists and by paleontologists, and recently ecologists have adopted the use of stable isotopes to measure ecosystem patterns and processes. To date, animal physiological ecologists have made minimal use of naturally occurring stable isotopes as tracers. Here we provide a review of the current and potential uses of naturally occurring stable isotopes in animal physiological ecology. We outline the physical and biological processes that lead to variation in isotopic abundance in plants and animals. We summarize current uses in animal physiological ecology (diet reconstruction and animal movement patterns), and suggest areas of research where the use of stable isotopes can be fruitful (protein balance and turnover and the allocation of dietary nutrients). We argue that animal physiological ecologists can benefit from including the measurement of naturally occurring stable isotopes in their battery of techniques. We also argue that animal physiologists can make an important contribution to the emerging field of stable isotopes in biology by testing experimentally the plethora of assumptions upon which the techniques rely.

High-precision continuous-flow isotope ratio mass spectrometry

Although high-precision isotope determinations are routine in many areas of natural science, the instrument principles for their measurements have remained remarkably unchanged for four decades. The introduction of continuous-flow techniques to isotope ratio mass spectrometry (IRMS) instrumentation has precipitated a rapid expansion in capabilities for high-precision measurement of C, N, O, S, and H isotopes in the 1990s. Elemental analyzers, based on the flash combustion of solid organic samples, are interfaced to IRMS to facilitate routine C and N isotopic analysis of unprocessed samples. Gas/liquid equilibrators have automated O and H isotopic analysis of water in untreated aqueous fluids as complex as urine. Automated cryogenic concentrators permit analysis at part-per-million concentrations in environmental samples. Capillary gas chromatography interfaced to IRMS via on-line microchemistry facilitates compound-specific isotope analysis (CSIA) for purified organic analytes of 1 nmol of C, N, or O. GC-based CSIA for hydrogen and liquid chromatography-based interfaces to IRMS have both been demonstrated, and continuing progress promises to bring these advances to routine use. Automated position-specific isotope analysis (PSIA) using noncatalytic pyrolysis has been shown to produce fragments without appreciable carbon scrambling or major isotopic fractionation, and shows great promise for intramolecular isotope ratio analysis. Finally, IRMS notation and useful elementary isotopic relationships derived from the fundamental mass balance equation are presented.

High-precision position-specific isotope analysis

Intramolecular carbon isotope distributions reflect details of the origin of organic compounds and may record the status of complex systems, such as environmental or physiological states. A strategy is reported here for high-precision determination of 13C/12C ratios at specific positions in organic compounds separated from complex mixtures. Free radical fragmentation of methyl palmitate, a test compound, is induced by an open tube furnace. Two series of peaks corresponding to bond breaking from each end of the molecule are analyzed by isotope ratio mass spectrometry and yield precisions of SD(delta-13C) < 0.4 per thousand. Isotope labeling in the carboxyl, terminal, and methyl positions demonstrates the absence of rearrangement during activation and fragmentation. Negligible isotopic fractionation was observed as degree of fragmentation was adjusted by changing pyrolysis temperature. [1-13C]methyl palmitate with overall delta-13C = 4.06 per thousand, yielded values of +457 per thousand for the carboxyl position, in agreement with expectations from the dilution, and an average of -27.95 per thousand for the rest of the molecule, corresponding to -27.46 per thousand for the olefin series. These data demonstrate the feasibility of automated high-precision position-specific analysis of carbon for molecules contained in complex mixtures.

Carbon isotopic fractionation associated with lipid biosynthesis by a cyanobacterium: relevance for interpretation of biomarker records

For the cyanobacterium Synechocystis UTEX 2470, grown photoautotrophically to a logarithmic stage of growth, the total lipid extract is depleted in 13C by 4.8% relative to average biomass. Depletions observed for acetogenic (straight-chain) lipids range from 7.6 (hexadecanoic acid) to 9.9% (a C16 n-alkyl chain bound in a polar-lipid fraction), with a mass-weighted average of 9.1%. Polyisoprenoid lipids fall into two isotopic groups, with phytol, diplopterol, and diploptene depleted by 6.4-6.9% and bishomohopanol (produced from the extracts by the preparative degradation of bacteriohopanepolyol) depleted by 8.4%. Analysis of the pattern of depletions indicates that two carbon positions in each C5 biomonomer leading to polyisoprenoid products are probably depleted in 13C relative to average biomass. The depletion of bacteriohopanepolyol relative to other polyisoprenoids can be ascribed to changes that occur over the life of each cell: (1) the 13C content of carbon flowing to lipid biosynthesis decreases as the cell size increases and (2) a greater proportion of the bacteriohopanepolyol which, unlike other polyisoprenoids, is present mainly in the cytoplasm rather than in membranes and is synthesized when cells are larger. Chlorophyll a is depleted relative to average biomass by O.7%. Given the observed depletion of 13C in phytol, the heteroaromatic, chlorophyllide portion of chlorophyll must be enriched in 13C by 2.7%. This enrichment is large relative to that in chlorophyllides produced by eukaryotes and may be related to a parallel enrichment of 13C in cyanobacterial glutamic acid. As in many previous investigations of cyanobacterial lipids, long-chain n-alkanes (C22-C29) are found in the extracts. They are, however, enriched in 13C relative to biomass and have isotopic compositions suggesting that they are contaminants of petrochemical origin. Available results indicate that cyanobacterial lipids will be depleted relative to dissolved CO2 that has served as a carbon source by 22-30% and that a wider range of depletions will be characteristic of eukaryotic products. The absence of long-chain n-alkanes in cyanobacteria reduces the possibility that petroleum ever formed from pre-eukaryotic sedimentary debris.

Elongation of exogenous fatty acids by the bioluminescent bacterium Vibrio harveyi

Bioluminescent bacteria require myristic acid (C14:0) to produce the myristaldehyde substrate of the light-emitting luciferase reaction. Since both endogenous and exogenous C14:0 can be used for this purpose, the metabolism of exogenous fatty acids by luminescent bacteria has been investigated. Both Vibrio harveyi and Vibrio fischeri incorporated label from [1-14C]myristic acid (C14:0) into phospholipid acyl chains as well as into CO2. In contrast, Photobacterium phosphoreum did not exhibit phospholipid acylation or beta-oxidation using exogenous fatty acids. Unlike Escherichia coli, the two Vibrio species can directly elongate fatty acids such as octanoic (C8:0), lauric (C12:0), and myristic acid, as demonstrated by radio-gas liquid chromatography. The induction of bioluminescence in late exponential growth had little effect on the ability of V. harveyi to elongate fatty acids, but it did increase the amount of C14:0 relative to C16:0 labeled from [14C]C8:0. This was not observed in a dark mutant of V. harveyi that is incapable of supplying endogenous C14:0 for luminescence. Cerulenin preferentially decreased the labeling of C16:0 and of unsaturated fatty acids from all 14C-labeled fatty acid precursors as well as from [14C]acetate, suggesting that common mechanisms may be involved in elongation of fatty acids from endogenous and exogenous sources. Fatty acylation of the luminescence-related synthetase and reductase enzymes responsible for aldehyde synthesis exhibited a chain-length preference for C14:0, which also was indicated by reverse-phase thin-layer chromatography of the acyl groups attached to these enzymes. The ability of V. harveyi to activate and elongate exogenous fatty acids may be related to an adaptive requirement to metabolize intracellular C14:0 generated by the luciferase reaction during luminescence development.

Utilization of alpha-ketoisocaproate for synthesis of hepatic export proteins and peripheral proteins in normal and cirrhotic subjects

The ratio R, defined as (percent of dose of 14C)/(percent of dose of 3H) in the leucine of plasma fibrinogen, albumin, immunoglobulin G (IgG), red cell globin, and salivary mucin, was measured in 7 normal adults and in 5 cirrhotic patients during continuous intragastric infusion of 1-14C-labeled alpha-ketoisocaproate (KIC) and 3H-labeled leucine. The ratio R measured in whole body protein has been shown in rat experiments to be a measure of the nutritional efficiency of KIC relative to leucine. In normal subjects, R in albumin and fibrinogen became constant (0.63 +/- 0.05) after the third hour and were indistinguishable from one another. The ratio R in IgG was similar and constant. The ratio R in plasma leucine (0.62 +/- 0.06) was significantly lower than R in mucin (0.86 +/- 0.04) or globin (0.73 +/- 0.04), indicating that these latter proteins derive a significant fraction of their leucine from KIC transaminated locally, rather than from circulating leucine. Results in 5 cirrhotic patients were the same, except that R in IgG and R in globin were significantly increased. Thus, cirrhosis does not alter the efficiency, relative to leucine, with which oral KIC is used for synthesis of export proteins by the liver, but increases the efficiency with which it is used for the synthesis of some proteins peripherally.