Quantification of Deuterium Isotopomers of Tree-Ring Cellulose Using Nuclear Magnetic Resonance

The marriage between stable isotope ecology and plant metabolomics - new perspectives for metabolic flux analysis and the interpretation of ecological archives

Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment-metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.

Metabolism is a major driver of hydrogen isotope fractionation recorded in tree-ring glucose of Pinus nigra

Stable isotope abundances convey valuable information about plant physiological processes and underlying environmental controls. Central gaps in our mechanistic understanding of hydrogen isotope abundances impede their widespread application within the plant and biogeosciences. To address these gaps, we analysed intramolecular deuterium abundances in glucose of Pinus nigra extracted from an annually resolved tree-ring series (1961-1995). We found fractionation signals (i.e. temporal variability in deuterium abundance) at glucose H¹ and H² introduced by closely related metabolic processes. Regression analysis indicates that these signals (and thus metabolism) respond to drought and atmospheric CO₂ concentration beyond a response change point. They explain ≈ 60% of the whole-molecule deuterium variability. Altered metabolism is associated with below-average yet not exceptionally low growth. We propose the signals are introduced at the leaf level by changes in sucrose-to-starch carbon partitioning and anaplerotic carbon flux into the Calvin-Benson cycle. In conclusion, metabolism can be the main driver of hydrogen isotope variation in plant glucose.

Anaplerotic flux into the Calvin-Benson cycle: hydrogen isotope evidence for in vivo occurrence in C3 metabolism

As the central carbon uptake pathway in photosynthetic cells, the Calvin-Benson cycle is among the most important biochemical cycles for life on Earth. A carbon flux of anaplerotic origin (i.e. through the chloroplast-localized oxidative branch of the pentose phosphate pathway) into the Calvin-Benson cycle was proposed recently. Here, we measured intramolecular deuterium abundances in leaf starch of Helianthus annuus grown at varying ambient CO₂ concentrations, C_a . Additionally, we modelled deuterium fractionations expected for the anaplerotic pathway and compared modelled with measured fractionations. We report deuterium fractionation signals at H¹ and H² of starch glucose. Below a C_a change point, these signals increase with decreasing C_a consistent with modelled fractionations by anaplerotic flux. Under standard conditions (C_a  = 450 ppm corresponding to intercellular CO₂ concentrations, C_i , of 328 ppm), we estimate negligible anaplerotic flux. At C_a  = 180 ppm (C_i  = 140 ppm), more than 10% of the glucose-6-phosphate entering the starch biosynthesis pathway is diverted into the anaplerotic pathway. In conclusion, we report evidence consistent with anaplerotic carbon flux into the Calvin-Benson cycle in vivo. We propose the flux may help to: maintain high levels of ribulose 1,5-bisphosphate under source-limited growth conditions to facilitate photorespiratory nitrogen assimilation required to build-up source strength; and counteract oxidative stress.

Global CO2 fertilization of Sphagnum peat mosses via suppression of photorespiration during the twentieth century

Natural peatlands contribute significantly to global carbon sequestration and storage of biomass, most of which derives from Sphagnum peat mosses. Atmospheric CO₂ levels have increased dramatically during the twentieth century, from 280 to > 400 ppm, which has affected plant carbon dynamics. Net carbon assimilation is strongly reduced by photorespiration, a process that depends on the CO₂ to O₂ ratio. Here we investigate the response of the photorespiration to photosynthesis ratio in Sphagnum mosses to recent CO₂ increases by comparing deuterium isotopomers of historical and contemporary Sphagnum tissues collected from 36 peat cores from five continents. Rising CO₂ levels generally suppressed photorespiration relative to photosynthesis but the magnitude of suppression depended on the current water table depth. By estimating the changes in water table depth, temperature, and precipitation during the twentieth century, we excluded potential effects of these climate parameters on the observed isotopomer responses. Further, we showed that the photorespiration to photosynthesis ratio varied between Sphagnum subgenera, indicating differences in their photosynthetic capacity. The global suppression of photorespiration in Sphagnum suggests an increased net primary production potential in response to the ongoing rise in atmospheric CO₂, in particular for mire structures with intermediate water table depths.

CO2 fertilization of Sphagnum peat mosses is modulated by water table level and other environmental factors

Sphagnum mosses account for most accumulated dead organic matter in peatlands. Therefore, understanding their responses to increasing atmospheric CO₂ is needed for estimating peatland C balances under climate change. A key process is photorespiration: a major determinant of net photosynthetic C assimilation that depends on the CO₂ to O₂ ratio. We used climate chambers to investigate photorespiratory responses of Sphagnum fuscum hummocks to recent increases in atmospheric CO₂ (from 280 to 400 ppm) under different water table, temperature, and light intensity levels. We tested the photorespiratory variability using a novel method based on deuterium isotopomers (D6^S /D6^R ratio) of photosynthetic glucose. The effect of elevated CO₂ on photorespiration was highly dependent on water table. At low water table (-20 cm), elevated CO₂ suppressed photorespiration relative to C assimilation, thus substantially increasing the net primary production potential. In contrast, a high water table (~0 cm) favored photorespiration and abolished this CO₂ effect. The response was further tested for Sphagnum majus lawns at typical water table levels (~0 and -7 cm), revealing no effect of CO₂ under those conditions. Our results indicate that hummocks, which typically experience low water table levels, benefit from the 20th century's increase in atmospheric CO₂ .

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

Isotope ratio monitoring by ¹³C NMR spectrometry (irm-¹³C NMR) provides the complete ¹³C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of ¹³C natural abundance values (50‰), irm-¹³C NMR requires a 1‰ accuracy and thus highly quantitative analysis by ¹³C NMR. Until now, the conventional strategy to determine the position-specific abundance x_i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and ¹³C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform ¹³C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative ¹H NMR pulse sequence (named DWET) with a ¹³C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T₁, which forms a serious limitation for irm-¹³C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T₁ variations. Their performance is evaluated on the determination of the ¹³C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-¹³C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades

Measurements of carbon isotope contents of plant organic matter provide important information in diverse fields such as plant breeding, ecophysiology, biogeochemistry and paleoclimatology. They are currently based on ¹³C/¹²C ratios of specific, whole metabolites, but we show here that intramolecular ratios provide higher resolution information. In the glucose units of tree-ring cellulose of 12 tree species, we detected large differences in ¹³C/¹²C ratios (>10‰) among carbon atoms, which provide isotopically distinct inputs to major global C pools, including wood and soil organic matter. Thus, considering position-specific differences can improve characterisation of soil-to-atmosphere carbon fluxes and soil metabolism. In a Pinus nigra tree-ring archive formed from 1961 to 1995, we found novel ¹³C signals, and show that intramolecular analysis enables more comprehensive and precise signal extraction from tree rings, and thus higher resolution reconstruction of plants’ responses to climate change. Moreover, we propose an ecophysiological mechanism for the introduction of a ¹³C signal, which links an environmental shift to the triggered metabolic shift and its intramolecular ¹³C signature. In conclusion, intramolecular ¹³C analyses can provide valuable new information about long-term metabolic dynamics for numerous applications.

On the contributions of photorespiration and compartmentation to the contrasting intramolecular 2H profiles of C3 and C4 plant sugars

Compartmentation of C₄ photosynthetic biochemistry into bundle sheath (BS) and mesophyll (M) cells, and photorespiration in C₃ plants is predicted to have hydrogen isotopic consequences for metabolites at both molecular and site-specific levels. Molecular-level evidence was recently reported (Zhou et al., 2016), but evidence at the site-specific level is still lacking. We propose that such evidence exists in the contrasting ²H distribution profiles of glucose samples from naturally grown C₃, C₄ and CAM plants: photorespiration contributes to the relative ²H enrichment in H⁵ and relative ²H depletion in H¹ & H⁶ (the average of the two pro-chiral Hs and in particular H^6,pro-R) in C₃ glucose, while ²H-enriched C₃ mesophyll cellular (chloroplastic) water most likely contributes to the enrichment at H⁴; export of (transferable hydrogen atoms of) NADPH from C₄ mesophyll cells to bundle sheath cells (via the malate shuttle) and incorporation of ²H-relatively unenriched BS cellular water contribute to the relative depletion of H⁴ & H⁵ respectively; shuttling of triose-phosphates (PGA: phosphoglycerate dand DHAP: dihydroacetone phosphate) between C₄ bundle sheath and mesophyll cells contributes to the relative enrichment in H¹ & H⁶ (in particular H^6,pro-R) in C₄ glucose.

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.

The new face of isotopic NMR at natural abundance

The most widely used method for isotope analysis at natural abundance is isotope ratio monitoring by Mass Spectrometry (irm-MS) which provides bulk isotopic composition in ² H, ¹³ C, ¹⁵ N, ¹⁸ O or ³⁴ S. However, in the 1980s, the direct access to Site-specific Natural Isotope Fractionation by Nuclear Magnetic Resonance (SNIF-NMR^TM ) was immediately recognized as a powerful technique to authenticate the origin of natural or synthetic products. The initial - and still most popular - application consisted in detecting the chaptalization of wines by irm-² H NMR. The approach has been extended to a wide range of methodologies over the last decade, paving the way to a wide range of applications, not only in the field of authentication but also to study metabolism. In particular, the emerging irm-¹³ C NMR approach delivers direct access to position-specific ¹³ C isotope content at natural abundance. After highlighting the application scope of irm-NMR (² H and ¹³ C), this article describes the major improvements which made possible to reach the required accuracy of 1‰ (0.1%) in irm-¹³ C NMR. The last part of the manuscript summarizes the different steps to perform isotope analysis as a function of the sample properties (concentration, peak overlap) and the kind of targeted isotopic information (authentication, affiliation). Copyright © 2016 John Wiley & Sons, Ltd.

Detecting long-term metabolic shifts using isotopomers: CO2-driven suppression of photorespiration in C3 plants over the 20th century

Terrestrial vegetation currently absorbs approximately a third of anthropogenic CO2 emissions, mitigating the rise of atmospheric CO2. However, terrestrial net primary production is highly sensitive to atmospheric CO2 levels and associated climatic changes. In C3 plants, which dominate terrestrial vegetation, net photosynthesis depends on the ratio between photorespiration and gross photosynthesis. This metabolic flux ratio depends strongly on CO2 levels, but changes in this ratio over the past CO2 rise have not been analyzed experimentally. Combining CO2 manipulation experiments and deuterium NMR, we first establish that the intramolecular deuterium distribution (deuterium isotopomers) of photosynthetic C3 glucose contains a signal of the photorespiration/photosynthesis ratio. By tracing this isotopomer signal in herbarium samples of natural C3 vascular plant species, crops, and a Sphagnum moss species, we detect a consistent reduction in the photorespiration/photosynthesis ratio in response to the ∼100-ppm CO2 increase between ∼1900 and 2013. No difference was detected in the isotopomer trends between beet sugar samples covering the 20th century and CO2 manipulation experiments, suggesting that photosynthetic metabolism in sugar beet has not acclimated to increasing CO2 over >100 y. This provides observational evidence that the reduction of the photorespiration/photosynthesis ratio was ca. 25%. The Sphagnum results are consistent with the observed positive correlations between peat accumulation rates and photosynthetic rates over the Northern Hemisphere. Our results establish that isotopomers of plant archives contain metabolic information covering centuries. Our data provide direct quantitative information on the "CO2 fertilization" effect over decades, thus addressing a major uncertainty in Earth system models.

Elucidating turnover pathways of bioactive small molecules by isotopomer analysis: the persistent organic pollutant DDT

The persistent organic pollutant DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane) is still indispensable in the fight against malaria, although DDT and related compounds pose toxicological hazards. Technical DDT contains the dichloro congener DDD (1-chloro-4-[2,2-dichloro-1-(4-chlorophenyl)ethyl]benzene) as by-product, but DDD is also formed by reductive degradation of DDT in the environment. To differentiate between DDD formation pathways, we applied deuterium NMR spectroscopy to measure intramolecular deuterium distributions (2H isotopomer abundances) of DDT and DDD. DDD formed in the technical DDT synthesis was strongly deuterium-enriched at one intramolecular position, which we traced back to 2H/1H fractionation of a chlorination step in the technical synthesis. In contrast, DDD formed by reductive degradation was strongly depleted at the same position, which was due to the incorporation of 2H-depleted hydride equivalents during reductive degradation. Thus, intramolecular isotope distributions give mechanistic information on reaction pathways, and explain a puzzling difference in the whole-molecule 2H/1H ratio between DDT and DDD. In general, our results highlight that intramolecular isotope distributions are essential to interpret whole-molecule isotope ratios. Intramolecular isotope information allows distinguishing pathways of DDD formation, which is important to identify polluters or to assess DDT turnover in the environment. Because intramolecular isotope data directly reflect isotope fractionation of individual chemical reactions, they are broadly applicable to elucidate transformation pathways of small bioactive molecules in chemistry, physiology and environmental science.

Stable isotopes in tree rings: towards a mechanistic understanding of isotope fractionation and mixing processes from the leaves to the wood

The mechanistic understanding of isotope fractionation processes is increasing but we still lack detailed knowledge of the processes that determine the isotopic composition of the tree-ring archive over the long term. Especially with regard to the path from leaf photosynthate production to wood formation, post-assimilation fractionations/processes might cause at least a partial decoupling between the leaf isotope signals that record processes such as stomatal conductance, transpiration and photosynthesis, and the wood or cellulose signals that are stored in the paleophysiological record. In this review, we start from the rather well understood processes at the leaf level such as photosynthetic carbon isotope fractionation, leaf water evaporative isotope enrichment and the issue of the isotopic composition of inorganic sources (CO2 and H2O), though we focus on the less explored 'downstream' processes related to metabolism and transport. We further summarize the roles of cellulose and lignin as important chemical constituents of wood, and the processes that determine the transfer of photosynthate (sucrose) and associated isotopic signals to wood production. We cover the broad topics of post-carboxylation carbon isotope fractionation and of the exchange of organic oxygen with water within the tree. In two case studies, we assess the transfer of carbon and oxygen isotopic signals from leaves to tree rings. Finally we address the issue of different temporal scales and link isotope fractionation at the shorter time scale for processes in the leaf to the isotopic ratio as recorded across longer time scales of the tree-ring archive.

ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach

Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/.

Deuterium incorporation in biomass cell wall components by NMR analysis

A commercially available deuterated kale sample was analyzed for deuterium incorporation by ionic liquid solution (2)H and (1)H nuclear magnetic resonance (NMR). This protocol was found to effectively measure the percent deuterium incorporation at 33%, comparable to the 31% value determined by combustion. The solution NMR technique also suggested by a qualitative analysis that deuterium is preferentially incorporated into the carbohydrate components of the kale sample.

Stable hydrogen isotope ratios of lignin methoxyl groups as a paleoclimate proxy and constraint of the geographical origin of wood

Stable isotope ratios of organic compounds are valuable tools for determining the geographical origin, identity, authenticity or history of samples from a vast range of sources such as sediments, plants and animals, including humans. Hydrogen isotope ratios (delta(2)H values) of methoxyl groups in lignin from wood of trees grown in different geographical areas were measured using compound-specific pyrolysis isotope ratio mass spectrometry analysis. Lignin methoxyl groups were depleted in (2)H relative to both meteoric water and whole wood. A high correlation (r(2) = 0.91) was observed between the delta(2)H values of the methoxyl groups and meteoric water, with a relatively uniform fractionation of -216 +/- 19 per thousand recorded with respect to meteoric water over a range of delta(2)H values from -110 in northern Norway to +20 per thousand in Yemen. Thus, woods from northern latitudes can be clearly distinguished from those from tropical regions. By contrast, the delta(2)H values of bulk wood were only relatively poorly correlated (r(2) = 0.47) with those of meteoric water. Measurement of the delta(2)H values of lignin methoxyl groups is potentially a powerful tool that could be of use not only in the constraint of the geographical origin of lignified material but also in paleoclimate, food authenticity and forensic investigations.