Tracking stable isotope enrichment in tree seedlings with solid-state NMR spectroscopy

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Using stable isotope labeling approach and two dimensional correlation spectroscopy to explore the turnover cycles of different carbon structures in extracellular polymeric substances

Extracellular polymeric substances (EPS) from activated sludge comprise many organic constituents with polysaccharides and proteins as the main components of two different functionalities. Despite a number of previous EPS studies, a fundamental question remained unanswered, namely, whether the different EPS components would have the same turnover cycle (i.e., formation/dissolution) in biological wastewater treatment systems. In this study, we employed a stable isotope labeling approach based on isotope-enriched substrates (i.e., ¹³C-glucose and ¹⁵NH₄Cl) to examine the potential discrepancies in the turnover cycles among different major EPS constituents. Our results, based on substrate consumption in a batch bioreactor, evidenced the existence of differences in carbon and nitrogen cycles within bulk EPS with an earlier replenishment of organic carbon relative to organic nitrogen. The changes in the 13C nuclear magnetic resonance (13C NMR) spectra of EPS with operation clarified the relative differences in the turnover periods among several identified EPS structures with different chemical functionalities. Two-dimensional correlation spectroscopy (2D-COS) on the 13C NMR spectra further showed that the substrate-assimilated carbon functional groups appear to preferably formed within bulk EPS in the order of O-alkyl carbons > amides > α amino acids > aliphatic carbons. This study provides a novel insight into the dissimilar formation rates of different EPS structures after substrate assimilation. This isotope labeling approach can be further applied to determine the mass balance among the substrate, biomass, and bound/soluble EPS within activated sludge systems.

Diurnal Variation in Nonstructural Carbohydrate Storage in Trees: Remobilization and Vertical Mixing

Nonstructural carbohydrate (NSC) storage plays a critical role in tree function and survival, but understanding and predicting local NSC storage dynamics is challenging because NSC storage pools are dispersed throughout the complex architecture of trees and continuously exchange carbon between source and sink organs at different time scales. To address these knowledge gaps, characterization and understanding of NSC diel variation are necessary. Here, we analyzed diurnal NSC dynamics in the overall architecture of almond (Prunus dulcis) trees. We also analyzed the allocation of newly assimilated carbon using isotopic labeling. We show that both components of NSC (i.e. soluble carbohydrates and starch) are highly dynamic at the diurnal time scale and that these trends are influenced by tissue type, age, and/or position within the canopy. In leaves, starch reserves can be depleted completely during the night, while woody tissue starch levels may vary by more than 50% over a daily cycle. Recently assimilated carbon showed a dispersed downward allocation across the entire tree. NSC diurnal fluctuations within the tree's structure in combination with dispersed carbon allocation patterns provide evidence for the presence of vertical mixing and suggest that the xylem acts as a secondary NSC redistribution pathway.

Stress differentially causes roots of tree seedlings to exude carbon

How carbon (C) flows through plants into soils is poorly understood. Carbon exuded comes from a pool of non-structural carbohydrates (NSC) in roots. Simple models of diffusion across concentration gradients indicate that the more C in roots, the more C should be exuded from roots. However, the mechanisms underlying the accumulation and loss of C from roots may differ depending on the stress experienced by plants. Thus, stress type may influence exudation independent of NSC. We tested this hypothesis by examining the relationship between NSC in fine roots and exudation of organic C in aspen (Populus tremuloides Michx.) seedlings after exposure to shade, cold soils and drought in a controlled environment. Fine root concentrations of NSC varied by treatment. Mass-specific C exudation increased with increasing fine root sugar concentration in all treatments, but stress type affected exudation independently of sugar concentration. Seedlings exposed to cold soils exuded the most C on a per mass basis. Through 13C labeling, we also found that stressed seedlings allocated relatively more new C to exudates than roots compared with unstressed seedlings. Stress affects exudation of C via mechanisms other than changes in root carbohydrate availability.

Template-free synthesis of a porous organic-inorganic hybrid tin(IV) phosphonate and its high catalytic activity for esterification of free fatty acids

Here we have synthesized an organic-inorganic hybrid mesoporous tin phosphonate monolith (MLSnP-1) with crystalline pore walls by a template-free sol-gel route. N2 sorption analysis shows Brunauer-Emmett-Teller (BET) surface area of 347 m2 g(-1). Wide-angle powder X-ray diffraction (PXRD) pattern shows few broad diffraction peaks indicating crystalline pore wall of the material. High-resolution transmission electron microscopic (HR TEM) image further reveals the crystal fringes on the pore wall. Framework bonding and local environment around phosphorus and carbon were examined by Fourier transform infrared (FT IR) spectroscopy and solid-state MAS NMR spectroscopy. The material exhibits remarkable catalytic activity for esterification of long chain fatty acids under mild reaction conditions at room temperature.