Biosynthetic control of the natural abundance of carbon 13 at specific positions within fatty acids in Saccharomyces cerevisiae. Isotopic fractionation in lipid synthesis as evidence for peroxisomal regulation

Organic Geochemical Characteristics and Organic Matter Enrichment of the Upper Permian Longtan Formation Black Shale in Southern Anhui Province, South China

Although previous studies have yielded valuable insights into shale gas reservoirs, a comprehensive understanding of the organic geochemical characteristics and organic matter enrichment of marine-continental transitional shale has yet to be achieved. The Longtan Formation transitional shales were extensively deposited in Southern Anhui Province, South China, during the Late Permian. Our analysis of twenty-two rock samples from one core (Gangdi-1 well) and two outcrops (Daoshanchong outcrop and Changqiao outcrop) revealed that the Longtan Formation shale extracts exhibit a wide range of C₁₁-C₃₅n-alkanes and acyclic isoprenoids, with unimodal, bimodal, and multimodal distributions. The carbon peak ranges from nC₁₅ to nC₂₄, with high quantities of medium-chain n-alkanes (nC₂₂-nC₂₅), indicating that the organic matter in Longtan Formation shale originates from a mixed source of higher plant debris and lower aquatic organisms. Our conclusion is supported by the ternary diagram of C₂₇-C₂₈-C₂₉ regular steranes and the variations of the δ¹³C values of C₁₅-C₃₂n-alkanes, which is higher than the corresponding value (<1.6‰) of n-alkanes from a single source. Furthermore, thermal maturity proxies based on organic petrography (R_o and T_max) and biomarkers, such as the ratios of C₃₁ 22S/(22S + 22R), C₂₉ 20S/(20S + 20R), and C₂₉ ββ/(αα + ββ), suggest that organic matter is in a mature stage of hydrocarbon generation. By analyzing the Pr/Ph ratio and pyrite morphology combined with a plot of total organic carbon (TOC) versus total sulfur (TS) and the Pr/nC₁₇-Ph/nC₁₈ diagram, we speculate that the Longtan Formation shales were chiefly developed in a dysoxic-to-oxic water environment. Finally, we establish depositional models of organic matter enrichment in deltaic and tidal flat-lagoon environments, emphasizing that the abundant mixed-sourced organic matter can significantly enhance primary productivity, and a higher sedimentation rate can distinctly shorten organic matter exposure time in the oxidized water environment, thereby promoting organic matter accumulation in such a setting.

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.

Non-statistical 13C Fractionation Distinguishes Co-incident and Divergent Steps in the Biosynthesis of the Alkaloids Nicotine and Tropine

During the biosynthesis of natural products, isotopic fractionation occurs due to the selectivity of enzymes for the heavier or lighter isotopomers. As only some of the positions in the molecule are implicated in a given reaction mechanism, position-specific fractionation occurs, leading to a non-statistical distribution of isotopes. This can be accessed by isotope ratio monitoring (13)C NMR spectrometry. The solanaceous alkaloids S-(-)-nicotine and hyoscyamine (atropine) are related in having a common intermediate, but downstream enzymatic steps diverge, providing a relevant test case to: (a) elucidate the isotopic affiliation between carbon atoms in the alkaloids and those in the precursors; (b) obtain information about the kinetic isotope effects of as yet undescribed enzymes, thus to make predictions as to their possible mechanism(s). We show that the position-specific (13)C/(12)C ratios in the different moieties of these compounds can satisfactorily be related to their known precursors and to the known kinetic isotope effects of enzymes involved in their biosynthesis, or to similar reaction mechanisms. Thus, the pathway to the common intermediate, N-methyl-Δ(1)-pyrrolinium, is seen to introduce similar isotope distribution patterns in the two alkaloids independent of plant species, whereas the remaining atoms of each target compound, which are of different origins, reflect their specific metabolic ancestry. We further demonstrate that the measured (13)C distribution pattern can be used to deduce aspects of the reaction mechanism of enzymes still to be identified.

Carbon sources and trophic relationships of ice seals during recent environmental shifts in the Bering Sea

Dramatic multiyear fluctuations in water temperature and seasonal sea ice extent and duration across the Bering-Chukchi continental shelf have occurred in this century, raising a pressing ecological question: Do such environmental changes alter marine production processes linking primary producers to upper trophic-level predators? We examined this question by comparing the blubber fatty acid (FA) composition and stable carbon isotope ratios of individual FA (δ¹³CFA) of adult ringed seals (Pusa hispida), bearded seals (Erignathus barbatus), spotted seals (Phoca largha), and ribbon seals (Histriophoca fasciata), collectively known as "ice seals," sampled during an anomalously warm, low sea ice period in 2002-2005 in the Bering Sea and a subsequent cold, high sea ice period in 2007-2010. δ¹³C(FA) values, used to estimate the contribution to seals of carbon derived from sea ice algae (sympagic production) relative to that derived from water column phytoplankton (pelagic production), indicated that during the cold period, sympagic production accounted for 62-80% of the FA in the blubber of bearded seals, 51-62% in spotted seals, and 21-60% in ringed seals. Moreover, the δ¹³CFA values of bearded seals indicated a greater incorporation of sympagic FAs during the cold period than the warm period. This result provides the first empirical evidence of an ecosystem-scale effect of a putative change in sympagic production in the Western Arctic. The FA composition of ice seals showed clear evidence of resource partitioning among ringed, bearded, and spotted seals, and little niche separation between spotted and ribbon seals, which is consistent with previous studies. Despite interannual variability, the FA composition of ringed and bearded seals showed little evidence of differences in diet between the warm and cold periods. The findings that sympagic production contributes significantly to food webs supporting ice seals, and that the contribution apparently is less in warm years with low sea ice, raise an important concern: Will the projected warming and continuing loss of seasonal sea ice in the Arctic, and the associated decline of organic matter input from sympagic production, be compensated for by pelagic production to satisfy both pelagic and benthic carbon and energy needs?

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

Tramadol, previously only known as a synthetic analgesic, has now been found in the bark and wood of roots of the African medicinal tree Nauclea latifolia. At present, no direct evidence is available as to the biosynthetic pathway of its unusual skeleton. To provide guidance as to possible biosynthetic precursors, we have adopted a novel approach of retro-biosynthesis based on the position-specific distribution of isotopes in the extracted compound. Relatively recent developments in isotope ratio monitoring by (13)C NMR spectrometry make possible the measurement of the nonstatistical position-specific natural abundance distribution of (13)C (δ(13)Ci) within the molecule with better than 1‰ precision. Very substantial variation in the (13)C positional distribution is found: between δ(13)Ci = -11 and -53‰. Distribution is not random and it is argued that the pattern observed can substantially be interpreted in relation to known causes of isotope fractionation in natural products. Thus, a plausible biosynthetic scheme based on sound biosynthetic principals of precursor-substrate relationships can be proposed. In addition, data obtained from the (18)O/(16)O ratios in the oxygen atoms of the compound add support to the deductions made from the carbon isotope analysis. This paper shows how the use of (13)C NMR at natural abundance can help with proposing a biosynthetic route to compounds newly found in nature or those difficult to tackle by conventional means.

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.

Multi-factorial in vivo stable isotope fractionation: causes, correlations, consequences and applications

Many physical and chemical processes in living systems are accompanied by isotope fractionation on H, C, N, O and S. Although kinetic or thermodynamic isotope effects are always the basis, their in vivo manifestation is often modulated by secondary influences. These include metabolic branching events or metabolite channeling, metabolite pool sizes, reaction mechanisms, anatomical properties and compartmentation of plants and animals, and climatological or environmental conditions. In the present contribution, the fundamentals of isotope effects and their manifestation under in vivo conditions are outlined. The knowledge about and the understanding of these interferences provide a potent tool for the reconstruction of physiological events in plants and animals, their geographical origin, the history of bulk biomass and the biosynthesis of defined representatives. It allows the use of isotope characteristics of biomass for the elucidation of biochemical pathways and reaction mechanisms and for the reconstruction of climatic, physiological, ecological and environmental conditions during biosynthesis. Thus, it can be used for the origin and authenticity control of food, the study of ecosystems and animal physiology, the reconstruction of present and prehistoric nutrition chains and paleaoclimatological conditions. This is demonstrated by the outline of fundamental and application-orientated examples for all bio-elements. The aim of the review is to inform (advanced) students from various disciplines about the whole potential and the scope of stable isotope characteristics and fractionations and to provide them with a comprehensive introduction to the literature on fundamental aspects and applications.

Evaluation of commercially available reagents as a reference material for intramolecular carbon isotopic measurements of acetic acid

RATIONALE

Recent advances in analytical techniques for the intramolecular carbon isotopic ratio measurement of some organic compounds have provided important information on carbon cycles in biochemistry, organic geochemistry and food chemistry. These advances have made it necessary to prepare intramolecular isotopic reference materials (RMs) to use for inter-laboratory calibration and/or inter-calibration among different analytical methods.

METHODS

We evaluated the feasibility of preparing RMs using commercially available reagents for intramolecular carbon isotopic ratio measurement of acetic acid. The intramolecular carbon isotopic distribution of nine acetic acid and four sodium acetate reagents was determined with high precision using off-line pyrolysis combined with gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). We also evaluated the potential alteration in the isotopic signature of acetic acid reagents by evaporation.

RESULTS

The intramolecular carbon isotopic distributions for the acetic acid and sodium acetate reagents were determined with a precision of better than 0.45‰. We found that the isotopic values of these reagents spanned the carbon isotopic range of acetic acid in biological and environmental samples. We also found that the isotope fractionation associated with the evaporation of acetic acid occurs solely on the methyl position, the carboxyl position being unaffected.

CONCLUSIONS

These commercially available reagents will be used as RMs in the future for inter-laboratory calibration and/or inter-calibration with another intramolecular isotopic measurement technique, namely quantitative (13) C NMR. In cases where acetic acid is being used as a RM, its storage must be carefully controlled to prevent evaporation.

Changes in tissue lipid and fatty acid composition of farmed rainbow trout in response to dietary camelina oil as a replacement of fish oil

Camelina oil (CO) replaced 50 and 100 % of fish oil (FO) in diets for farmed rainbow trout (initial weight 44 ± 3 g fish(-1)). The oilseed is particularly unique due to its high lipid content (40 %) and high amount of 18:3n-3 (α-linolenic acid, ALA) (30 %). Replacing 100 % of fish oil with camelina oil did not negatively affect growth of rainbow trout after a 12-week feeding trial (FO = 168 ± 32 g fish(-1); CO = 184 ± 35 g fish(-1)). Lipid and fatty acid profiles of muscle, viscera and skin were significantly affected by the addition of CO after 12 weeks of feeding. However, final 22:6n-3 [docosahexaenoic acid (DHA)] and 20:5n-3 [eicosapentaenoic acid (EPA)] amounts (563 mg) in a 75 g fillet (1 serving) were enough to satisfy daily DHA and EPA requirements (250 mg) set by the World Health Organization. Other health benefits include lower SFA and higher MUFA in filets fed CO versus FO. Compound-specific stable isotope analysis (CSIA) confirmed that the δ(13)C isotopic signature of DHA in CO fed trout shifted significantly compared to DHA in FO fed trout. The shift in DHA δ(13)C indicates mixing of a terrestrial isotopic signature compared to the isotopic signature of DHA in fish oil-fed tissue. These results suggest that ~27 % of DHA was synthesized from the terrestrial and isotopically lighter ALA in the CO diet rather than incorporation of DHA from fish meal in the CO diet. This was the first study to use CSIA in a feeding experiment to demonstrate synthesis of DHA in fish.

Isotopic biosignatures in carbonate-rich, cyanobacteria-dominated microbial mats of the Cariboo Plateau, B.C

Photosynthetic activity in carbonate-rich benthic microbial mats located in saline, alkaline lakes on the Cariboo Plateau, B.C. resulted in pCO2 below equilibrium and δ(13) CDIC values up to +6.0‰ above predicted carbon dioxide (CO2 ) equilibrium values, representing a biosignature of photosynthesis. Mat-associated δ(13) Ccarb values ranged from ~4 to 8‰ within any individual lake, with observations of both enrichments (up to 3.8‰) and depletions (up to 11.6‰) relative to the concurrent dissolved inorganic carbon (DIC). Seasonal and annual variations in δ(13) C values reflected the balance between photosynthetic (13) C-enrichment and heterotrophic inputs of (13) C-depleted DIC. Mat microelectrode profiles identified oxic zones where δ(13) Ccarb was within 0.2‰ of surface DIC overlying anoxic zones associated with sulphate reduction where δ(13) Ccarb was depleted by up to 5‰ relative to surface DIC reflecting inputs of (13) C-depleted DIC. δ(13) C values of sulphate reducing bacteria biomarker phospholipid fatty acids (PLFA) were depleted relative to the bulk organic matter by ~4‰, consistent with heterotrophic synthesis, while the majority of PLFA had larger offsets consistent with autotrophy. Mean δ(13) Corg values ranged from -18.7 ± 0.1 to -25.3 ± 1.0‰ with mean Δ(13) Cinorg-org values ranging from 21.1 to 24.2‰, consistent with non-CO2 -limited photosynthesis, suggesting that Precambrian δ(13) Corg values of ~-26‰ do not necessitate higher atmospheric CO2 concentrations. Rather, it is likely that the high DIC and carbonate content of these systems provide a non-limiting carbon source allowing for expression of large photosynthetic offsets, in contrast to the smaller offsets observed in saline, organic-rich and hot spring microbial mats.

Isotope fractionations in the biosynthesis of cell components by different fungi: a basis for environmental carbon flux studies

Abstract The isotope fractionation of carbon from substrates possessing different isotope ratios into fatty acids of polar lipids and amino acids was determined for four different fungi (Rhizopus arrhizus, Mortierella isabellina, Fusarium solani, Aspergillus niger). Carbon isotope ratios of fungi closely followed that of the substrates. Palmitic acid (C16:0), derived from phospholipids, did not display a large carbon isotope fractionation against the substrate. Stearic acid (C18:0), however, was depleted in (13)C against C16:0 in all strains. The desaturation of C18:0 to oleic acid (C18:1omega9) had little effect on the carbon isotope ratio. The subsequent desaturation of C18:1omega9 to linolic acid (C18:2omega6,9) enriched the resulting C18:2omega6,9 by +3.9 per thousand and varied little among strains. This result is important because C18:2omega6,9 is often used as a biomarker in environmental studies. Most amino acids were enriched in (13)C compared to the substrates, but isoleucine and lysine were close to the isotope ratio of the substrate and phenylalanine and leucine were depleted. Interestingly, the carbon isotope ratios of many amino acids differed significantly among different species. A discriminant analysis based on the isotope ratio of four amino acids (Thr, Ile, Phe, Val) resolved the two phyla in the first discriminant function and all four strains in the first two discriminant functions and confirmed a taxon-specific manner of isotope fractionation. The derived rules provide the basis for the use of stable isotopes in environmental studies to elucidate the role of fungi in the carbon flow in the environment.

Carbon isotopic fractionation in eider adipose tissue varies with fatty acid structure: implications for trophic studies

Carbon isotopic fractionation was investigated in fatty acids (FA) of adipose tissue and blood serum of threatened Steller's eiders (Polysticta stelleri) and spectacled eiders (Somateria fischeri) relative to the FA in their diets. Captive eiders were fed a known diet for 180 days with serum sampled at 60, 120 and 180 days immediately after a 12 fast; adipose was collected at 180 days. Essential FA (EFA) in the adipose showed varying degrees of isotope fractionation (0–4‰), depending on FA structure. The δ13C values of long-chain FA 20:5n-3 and 22:6n-3 did not differ from those in the diet, while those of 18:2n-6 and 18:3n-3 were ∼2‰ greater than in the diet. The δ13C values of free FA (FFA) in serum were not consistent within individuals or sampling dates; fractionation varied randomly, suggesting that FFA were arising from diet, rather than mobilization from adipose tissue. Discrimination factors were used in combination with a mixing model incorporating FA and lipid concentrations to estimate the diet of eiders fed a binary mixture with contrasting isotopic signatures. Diet estimates varied with FA but mean values closely approximated the actual proportions consumed. By tracking EFA, this study avoided the complications in interpretation arising from isotopic routing of carbon in bulk isotope analyses and serves as a basis for the development of compound-specific isotopic methods to trace dietary input in wild eiders. However, our understanding of the processes contributing to the variation in isotopic signatures of FA in nature is currently limited, and we recommend that future research directions focus on elucidating these mechanisms.

Tracing metabolic pathways of lipid biosynthesis in ectomycorrhizal fungi from position-specific 13C-labelling in glucose

Six position-specific (13)C-labelled isotopomers of glucose were supplied to the ectomycorrhizal fungi Suillus pungens and Tricholoma flavovirens. From the resulting distribution of (13)C among fungal PLFAs, the overall order and contribution of each glucose atom to fatty acid (13)C enrichment was: C6 (approximately 31%) > C5 (approximately 25%) > C1 (approximately 18%) > C2 (approximately 18%) > C3 (approximately 8%) > C4 (approximately 1%). These data were used to parameterize a metabolic model of the relative fluxes from glucose degradation to lipid synthesis. Our data revealed that a higher amount of carbon is directed to glycolysis than to the oxidative pentose phosphate pathway (60% and 40% respectively) and that a significant part flows through these pathways more than once (73%) due to the reversibility of some glycolysis reactions. Surprisingly, 95% of carbon cycled through glyoxylate prior to incorporation into lipids, possibly to consume the excess of acetyl-CoA produced during fatty acid turnover. Our approach provides a rigorous framework for analysing lipid biosynthesis in fungi. In addition, this approach could ultimately improve the interpretation of isotopic patterns at natural abundance in field studies.

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.

Tracing carbon flow in an arctic marine food web using fatty acid-stable isotope analysis

Global warming and the loss of sea ice threaten to alter patterns of productivity in arctic marine ecosystems because of a likely decline in primary productivity by sea ice algae. Estimates of the contribution of ice algae to total primary production range widely, from just 3 to >50%, and the importance of ice algae to higher trophic levels remains unknown. To help answer this question, we investigated a novel approach to food web studies by combining the two established methods of stable isotope analysis and fatty acid (FA) analysis--we determined the C isotopic composition of individual diatom FA and traced these biomarkers in consumers. Samples were collected near Barrow, Alaska and included ice algae, pelagic phytoplankton, zooplankton, fish, seabirds, pinnipeds and cetaceans. Ice algae and pelagic phytoplankton had distinctive overall FA signatures and clear differences in delta(13)C for two specific diatom FA biomarkers: 16:4n-1 (-24.0+/-2.4 and -30.7+/-0.8 per thousand, respectively) and 20:5n-3 (-18.3+/-2.0 and -26.9+/-0.7 per thousand, respectively). Nearly all delta(13)C values of these two FA in consumers fell between the two stable isotopic end members. A mass balance equation indicated that FA material derived from ice algae, compared to pelagic diatoms, averaged 71% (44-107%) in consumers based on delta(13)C values of 16:4n-1, but only 24% (0-61%) based on 20:5n-3. Our estimates derived from 16:4n-1, which is produced only by diatoms, probably best represented the contribution of ice algae relative to pelagic diatoms. However, many types of algae produce 20:5n-3, so the lower value derived from it likely represented a more realistic estimate of the proportion of ice algae material relative to all other types of phytoplankton. These preliminary results demonstrate the potential value of compound-specific isotope analysis of marine lipids to trace C flow through marine food webs and provide a foundation for future work.

Carbon Position-Specific Isotope Analysis of Alanine and Phenylalanine Analogues Exhibiting Nonideal Pyrolytic Fragmentation

Recent advances in gas chromatography combustion-isotope ratio mass spectrometry (GCC-IRMS) has made compound-specific isotope analysis routine, but reports on position-specific isotopic analysis are still scarce. On-line GC-pyrolysis (Py) coupled to GCC-IRMS is reported here for isolation and isotopic characterization of alaninol and phenethylamine, analogues of alanine and phenylalanine, respectively. Ideally, pyrolytic fragments will originate from unique sites within the parent molecule, and isotope ratios for each position within the parent can either be measured directly or calculated from fragment isotope ratios without substantially degrading the analytical precision. Alaninol pyrolysis yielded several fragments, of which CO and CH4 were used for isotope ratio calculations. Isotope labeling experiments showed that CO derived entirely from the C(1) position, while all three positions of alaninol contributed to CH4 (29.0 +/- 0.3% from C(1), 3.6 +/- 0.2% from C(2), and 66.9 +/- 1.1% from C(3)). We demonstrate iterative use of mass balance to calculate isotope ratios from all positions despite the nonideal positional fidelity of CH4. Pyrolysis of phenethylamine generated benzene and toluene fragments. Benzene derived entirely from C(ring), and toluene was proportionately formed from C(3) and C(ring). Relative intramolecular isotope ratios (Deltadelta13C) were calculated directly from delta13C of fragments or indirectly by mass balance. Though the C(3) isotope ratio was calculated from the benzene and toluene fragments, propagation of errors showed that the final precision of the determination was degraded due to the small contribution that C(3) makes to toluene. Samples of each amino acid from four different vendors showed natural variability between sources, especially at the C(1) position of alaninol (range of Deltadelta13C approximately 50 per thousand). The average precision was SD(Deltadelta13C) < 0.20 per thousand for directly measured positions of alaninol and phenethylamine. The precision of indirectly measured positions was poorer (SD(Deltadelta13C) = 0.94 per thousand for alaninol, 6.54 per thousand for phenethylamine) due to propagation of errors. These data demonstrate that GC-Py-GCC-IRMS data can be used to extract high-precision isotope ratios from amino acids despite nonideal positional fidelity in fragments and that natural intramolecular variability in delta13C can be used to distinguish different sources of amino acids.

The use of isotopic and lipid analysis techniques linking toluene degradation to specific microorganisms: applications and limitations

Phospholipid fatty acid (PLFA) analysis combined with (13)C-labeled tracers has been used recently as an environmental forensics tool to demonstrate microbial degradation of pollutants. This study investigated the effectiveness and limitations of this approach, applied to the biodegradation of toluene by five reference strains that express different aerobic toluene degradation pathways: Pseudomonas putida mt-2, P. putida F1, Burkholderia cepacia G4, B. pickettii PKO1, and P. mendocina KR1. The five strains were grown on mineral salts base medium amended with either 10 mM natural or [(13)C-ring]-labeled toluene. PLFA analysis showed that all five strains incorporated the toluene carbon into membrane fatty acids, as demonstrated by increases in the mass of fatty acids and their mass-spectrometry fragments for cells grown on (13)C-labeled toluene. Because of its ubiquitous presence and high abundance in bacteria, C16:0 fatty acid might be a useful biomarker for tracking contaminant degradation and (13)C flow. On the other hand, the (13)C-label (which was supplied at relatively high concentrations) generally exerted an inhibitory effect on fatty acid biosynthesis. Differences in fatty acid concentrations between cells grown on natural versus (13)C-labeled toluene would affect the interpretation of lipid profiles for microbial community analysis as indicated by principal component analysis of fatty acids. Therefore, caution should be exercised in linking lipid data with microbial population shifts in biodegradation experiments with (13)C-labeled tracers.

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.

Differential C isotope discrimination by fungi during decomposition of C(3)- and C(4)-derived sucrose

Stable isotope analysis is a major tool used in ecosystem studies to establish pathways and rates of C exchange between various ecosystem components. Little is known about isotopic effects of many such components, especially microbes. Here we report on the discovery of an unexpected pattern of C isotopic discrimination by basidiomycete fungi with far-reaching consequences for our understanding of isotopic processing in ecosystems where these microbes mediate material transfers across trophic levels. We measured fractionation effects on three ecologically relevant basidiomycete species under controlled laboratory conditions. Sucrose derived from C(3) and C(4) plants is fractionated differentially by these microbes in a taxon-specific manner. The differentiation between mycorrhizal and saprotrophic fungi observed in the field by others is not explained by intrinsic discrimination patterns. Fractionation occurs during sugar uptake and is sensitive to the nonrandom distribution of stable isotopes in the sucrose molecule. The balance between respiratory physiology and fermentative physiology modulates the degree of fractionation. These discoveries disprove the assumption that fungal C processing does not significantly alter the distribution of stable C isotopes and provide the basis for a reevaluation of ecosystem models based on isotopic evidence that involve C transfer across microbial interfaces. We provide a mechanism to account for the observed differential discrimination effects.

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.

Carbon isotopic fractionation in lipids from methanotrophic bacteria: relevance for interpretation of the geochemical record of biomarkers

Experiments with cultured aerobic methane oxidising bacteria confirm that their biomarker lipids will be significantly depleted in 13C compared to the substrate. The methanotrophic bacteria Methylococcus capsulatus and Methylomonas methanica, grown on methane and using the RuMP cycle for carbon assimilation, show maximum 13C fractionation of approximately 30% in the resultant biomass. In M. capsulatus, the maximum fractionation is observed in the earliest part of the exponential growth stage and decreases to approximately 16% as cells approach stationary phase. This change may be associated with a shift from the particulate form to the soluble form of the methane monooxygenase enzyme. Less than maximum fractionation is observed when cells are grown with reduced methane availability. Biomass of M. capsulatus grown on methanol was depleted by 9% compared to the substrate. Additional strong 13C fractionation takes place during polyisoprenoid biosynthesis in methanotrophs. The delta 13C values of individual hopanoid and steroid biomarkers produced by these organisms were as much as l0% more negative than total biomass. In individual cultures, squalene was 13C-enriched by as much as 14% compared to the triterpane skeleton of bacteriohopaneaminopentol. Much of the isotopic dispersion in lipid metabolites could be attributed to shifts in their relative abundances, combined with an overall reduction in fractionation during the growth cycle. In cells grown on methanol, where there was no apparent effect of growth stage on overall fractionation there were still significant isotopic differences between closely related lipids including a 5.3% difference between the hopane and 3 beta-methylhopane skeletons. Hopane and sterane polyisoprenoids were also 13C-depleted compared to fatty acids. These observations have significant implications for the interpretation of specific compound isotopic signatures now being measured for hydrocarbons and other lipids present in sediments and petroleum. In particular, biomarker lipids produced by a single organism do not necessarily have the same carbon isotopic composition.

Partial resolution of sources of n-alkanes in the saline portion of the Parachute Creek Member, Green River Formation (Piceance Creek Basin, Colorado)

Systematic variations in the 13C contents of individual extractable n-alkanes (C16-C29) can be modelled quantitatively and interpreted as indicating contributions from at least five distinct sources. These appear to be cyanobacterial (C16-C18, delta 13C = -37% vs PDB), phytoplanktonic (C16-C23, delta = -32%), chemoautotrophic bacterial (C20-C29, delta = -38%), phytoplanktonic or heterotrophic bacterial (C20-C29, delta = -30%), and vascular plants (C23-C29, delta = -29%). Hydrous pyrolysis of related kerogens yields large quantities of additional n-alkanes with different and much more uniform delta values. The latter materials are apparently derived from the thermolysis of aliphatic biopolymers whose presence in the Green River Oil Shale has been recognized visually.

An isotopic study of biogeochemical relationships between carbonates and organic carbon in the Greenhorn Formation

Carbon-isotopic compositions of total carbonate, inoceramid carbonate, micritic carbonate, secondary cements, total organic carbon, and geoporphyrins have been measured in 76 different beds within a 17-m interval of a core through the Greenhorn Formation, an interbedded limestone and calcareous shale unit of Cretaceous age (Cenomanian-Turonian) from the Western Interior Seaway of North America. Results are considered in terms of variations in the processes of primary production (which led to the biosynthesis of the molecular precursors of the geoporphyrins) and in secondary processes (those mediating the transformation of primary organic material into sedimentary total organic carbon). It is shown that the porphyrin isotopic record reflects primary isotopic variations more closely than the TOC isotopic record, and that, in these sediments, TOC is enriched in 13C relative to its primary precursor by 0.6 to 2.8%. This enrichment is attributed to isotope effects within the consumer foodweb and is associated with respiratory heterotrophy. Variations in this secondary enrichment are correlated with variations in the isotopic composition of marine carbonate. This correlation is attributed to effects of environmental changes on the marine foodweb. These may have included increased atmospheric oxygen associated with the Cenomanian-Turonian oceanic anoxic event. The isotopic fractionation associated with fixation of carbon by primary producers is observed to have varied by 1.5% during the interval of deposition. It is suggested that this change is due to a variation in the makeup of the community of primary producers and/or to a decrease in the atmospheric abundance of CO2 during the oceanic anoxic event.

Natural abundances of carbon isotopes in acetate from a coastal marine sediment

Measurements of the natural abundances of carbon isotopes were made in acetate samples isolated from the anoxic marine sediment of Cape Lookout Bight, North Carolina. The typical value of the total acetate carbon isotope ratio (delta 13C) was -16.1 +/- 0.2 per mil. The methyl and carboxyl groups were determined to be -26.4 +/- 0.3 and -6.0 +/- 0.3 per mil, respectively, for one sample. The isotopic composition of the acetate is thought to have resulted from isotopic discriminations that occurred during the cycling of that molecule. Measurements of this type, which have not been made previously in the natural environment, may provide information about the dominant microbial pathways in anoxic sediments as well as the processes that influence the carbon isotopic composition of biogenic methane from many sources.

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.