Metabolomics
Metabolomics is a field of "omics" research concerned with the comprehensive characterization of the small molecule metabolites in biological systems. It can provide an overview of the metabolic status and global biochemical events associated with a cellular or biological system. NMR spectroscopy and MS approaches are highly complementary, and use of both is often necessary for full molecular characterization
Published works
Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree
M. Sebastiana*, A. Gargallo-Garriga, J. Sardans, M. Pérez-Trujillo, F. Monteiro, A. Figueiredo, M. Maia, R. Nascimento, M. Sousa Silva, A. N. Ferreira, C. Cordeiro, A. P. Marques, .L Sousa, R. Malhó, J. Peñuelas
Scientific reports, 2021, 11, 1-16. DOI
Mycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.
31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees of a French Guiana Rainforest
A. Gargallo-Garriga,* J. Sardans, J. Llusià, G. Peguero, D. Asensio, R. Ogaya, I. Urbina, L. Van Langenhove, L. T. Verryckt, E. A. Courtois, C. Stahl, O.Grau, O. Urban, I. A. Janssens, P. Nolis, M. Pérez-Trujillo, T. Parella, J. Peñuelas
Molecules, 2020, 25, 3960. DOI
Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target 31P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. Results highlighted the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism.
Coping with iron limitation: a metabolomic study of Synechocystis sp. PCC 6803
A. Rivas-Ubach,* A. T. Poret-Peterson, J. Peñuelas, J. Sardans, M. Pérez-Trujillo, C. Legido-Quigley, M. Oravec, O. Urban, J. J. Elser
Acta Physiol Plant, 2018, 40: 28. DOI
Iron (Fe) is a key element for all living systems, especially for photosynthetic organisms because of its important role in the photosynthetic electron transport chain. Fe limitation in cyanobacteria leads to several physiological and morphological changes. However, the overall metabolic responses to Fe limitation are still poorly understood. In this study, we integrated elemental, stoichiometric, macromolecular, and metabolomic data to shed light on the responses of Synechocystis sp. PCC 6803, a non-N2-fixing freshwater cyanobacterium, to Fe limitation. This study represents an advance in understanding the stoichiometric, macromolecular, and metabolic strategies that cyanobacteria use to cope with Fe limitation. This information, moreover, may further understanding of changes in cyanobacterial functions under scenarios of Fe limitation in aquatic ecosystems.
Direct monitoring of exogenous γ-hydroxybutyric acid in body fluids by NMR spectroscopy
M. Palomino-Schätzlein, Y. Wang, A. D. Brailsford, T. Parella, D. A. Cowan, C. Legido-Quigley, M. Pérez-Trujillo*
Anal. Chem, 2017,89 (16), pp 8343–8350. DO
γ-Hydroxybutyric acid (GHB) is a popular drug increasingly associated to cases of drug-facilitated sexual assault (DFSA). Currently, expanding procedures of analysis and having forensic evidence of GHB intake at a long term are mandatory. Up to now, most studies have been performed using GC-MS and LC-MS as analytical platforms, which involve significant manipulation of the sample and, often, indirect measurements. In this work, procedures used in NMR-based metabolomics were applied to a GHB clinical trial on urine and serum. Detection, identification and quantification of the drug by NMR methods were surveyed, as well as the use of NMR-based metabolomics for the search of potential surrogate biomarkers of GHB consumption. Results demonstrated the suitability of NMR spectroscopy, as a robust nondestructive technique, to monitor (detect, identify and quantify) fast and directly exogenous GHB in almost intact body fluids, and its high potential in the search for metabolites associated to GHB intake.
Long-term fertilization determines different metabolomic profiles and responses in saplings of three rainforest tree species with different adult canopy position
A. Gargallo-Garriga,* S. J. Wright, J. Sardans, M. Pérez-Trujillo, M. Oravec, K. Večeřová,O. Urban, M. Fernández-Martínez, T. Parella, J. Peñuelas.
PLoS ONE, 2017;1-21. DOI
Tropical rainforests are frequently limited by soil nutrient availability. However, the response of the metabolic phenotypic plasticity of trees to an increase of soil nutrient availabilities is poorly understood. We expected that increases in the ability of a nutrient that limits some plant processes should be detected by corresponding changes in plant metabolome profile related to such processes. We studied the foliar metabolome of saplings of three abundant tree species in a 15 year field NPK fertilization experiment in a Panamanian rainforest. The largest differences were among species and explained 75% of overall metabolome variation.
Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota
A. Gargallo-Garriga*, J. Sardans, M. Pérez-Trujillo, A. Guenther, J. Llusià, L. Rico, J. Terradas, G. Farré-Armengo, I. Filella, T. Parella and J. Peñuelas
BMC Plant Biol. 2016; 16:78.DOI
The phyllospheric microbiota is assumed to play a key role in the metabolism of host plants. Its role in determining the epiphytic and internal plant metabolome, however, remains to be investigated. We analyzed the Liquid Chromatography-Mass Spectrometry (LC-MS) profiles of the epiphytic and internal metabolomes of the leaves and flowers of Sambucus nigra with and without external antibiotic treatment application. Obtained results suggest that anaerobic and/or facultative anaerobic bacteria were present in high numbers in the phyllosphere and in the apoplasts of S. nigra. The results also show that microbial communities play a significant role in the metabolomes of plant organs and could have more complex and frequent mutualistic, saprophytic, and/or parasitic relationships with internal plant metabolism than currently assumed.
Nuclear magnetic resonance (NMR) of goat follicular fluid shows different metabolic profiles among follicle size and female age
S. Soto, M. Pérez, M.G. Catalá, M. Roura, D. Izquierdo, T. Parella, M.T. Paramio
Proceedings of the 30th Annual Meeting of the Brazilian Embryo Technology Society (SBTE) and 32nd Meeting of the European Embryo Transfer Association (AETE); Barcelona, Spain, September 9th and 10th, 2016. Abstracts.
Animal Reproduction, 2016, 13 (3), 547-547. pdf
Oocytes recovered from prepubertal goats are highly heterogeneous in growth and grade of atresia which make them unpredictable for IVEP programs. In our laboratory we have observed that oocytes from 2 month-old goats obtained from > 3 mm follicles develop up to blastocyst stage at a similar percentage than oocytes from adult goats (18% and 21%, respectively), suggesting that the follicle development and the follicular fluid (FF) content are more relevant to oocyte competence than the age of the donor. The aim of this study was to characterize the FF metabolomic profile from different follicular environments. A High-resolution proton nuclear magnetic resonance (1H NMR)-based metabolomic study was carried out. Results showed that metabolomic profiles are different according to the follicle diameter and the female age. Some of these metabolomes could be related to the acquisition of oocyte competence and might be used as biomarkers of oocyte quality.
Opposite metabolic responses of shoots and roots to drought
A. Gargallo-Garriga*, J. Sardans, M. Pérez-Trujillo, A. Rivas-Ubach, M. Oravec, T. Parella and J. Peñuelas
Scientific reports, 2014, 4, Article number: 6829.DOI
Shoots and roots are autotrophic and heterotrophic organs of plants with different physiological functions. Do they have different metabolomes? Do their metabolisms respond differently to environmental changes such as drought? We used metabolomics and elemental analyses to answer these questions. First, we show that shoots and roots have different metabolomes and nutrient and elemental stoichiometries. Second, we show that the shoot metabolome is much more variable among species and seasons than is the root metabolome. Third, we show that the metabolic response of shoots to drought contrasts with that of roots; shoots decrease their growth metabolism (lower concentrations of sugars, amino acids, nucleosides, N, P, and K), and roots increase it in a mirrored response. Shoots are metabolically deactivated during drought to reduce the consumption of water and nutrients, whereas roots are metabolically activated to enhance the uptake of water and nutrients, together buffering the effects of drought, at least at the short term.
Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots
A. Gargallo-Garriga*, J. Sardans, M. Pérez-Trujillo, M. Oravec,O. Urban, A. Jentsch, J. Kreyling, C. Beierkuhnlein T. Parella and J. Peñuelas
New Phytologist, 2015, 207, 591–603.DOI
Plants in natural environments are increasingly being subjected to a combination of abiotic stresses, such as drought and warming, in many regions. The effects of each stress and the combination of stresses on the functioning of shoots and roots have been studied extensively, but little is known about the simultaneous metabolome responses of the different organs of the plant to different stresses acting at once. We studied the shift in metabolism and elemental composition of shoots and roots of two perennial grasses, Holcus lanatus and Alopecurus pratensis, in response to simultaneous drought and warming. These species responded differently to individual and simultaneous stresses. These responses were even opposite in roots and shoots. In plants exposed to simultaneous drought and warming, terpenes, catechin and indole acetic acid accumulated in shoots, whereas amino acids, quinic acid, nitrogenous bases, the osmoprotectants choline and glycine betaine, and elements involved in growth (N, P, K) accumulated in roots. Under drought, warming further increased the allocation of primary metabolic activity to roots and changed the composition of secondary metabolites in shoots. These results highlight the plasticity of plant metabolomes and stoichiometry, and the different complementary responses of shoots and roots to complex environmental conditions.
Drought enhances folivory by shifting foliar metabolomes in Quercus ilex trees
A. Rivas-Ubach*, A. Gargallo-Garriga, J. Sardans, M. Oravec, L. Mateu-Castell, M. Pérez-Trujillo,T. Parella, R. Ogaya, O. Urban and J. Peñuelas
New Phytologist, 2014, 202, 874–885.DOI
Plants respond to external environmental conditions such as drought or to the seasonal changes by shifting the foliar C:N:P:K stoichiometry and metabolome. Rates of folivory are usually associated with the water status of plants and/or concentrations of foliar nutrients, especially N, but studies have focused mainly on the concentrations of foliar nutrients or on particular foliar-specific metabolic families. Emerging ecometabolomic techniques allow the study of metabolomes, the total set of metabolites in an organism at a specific moment. This study attempts to integrate stoichiometric and metabolomic techniques, based on NMR spectroscopy and MS spectrometry, to understand the responses of Quercus ilex throughout seasons and under moderate experimental conditions of drought and how these responses affect rates of folivory. Our data suggest that the increase of sugars and flavonoids in Q. ilex leaves in droughted trees can lead to an increase in herbivorous attack, which implies an indirect relationship between increased drought and rate of folivory produced by metabolomic shifts. The present study represents an advance in understanding the potential cascade effects of drought at different trophic levels and their possible implications in the structure, function and evolution of ecosystems.
Ecometabolomics: Optimized NMR-based method
A. Rivas-Ubach*, M. Pérez-Trujillo*, J. Sardans, A. Gargallo-Garriga, T. Parella, J. Peñuelas
Methods in Ecology and Evolution, 2013, 4, 464–473. DOI
Metabolomics is allowing great advances in biological sciences and in particular Ecometabolomics (metabolomic approach for ecological studies). Ecometabolomics is a powerful tool that allows identifying changes in the metabolome of individuals of the same species associated to environmental changes, detecting and identifying biological markers.Here we describe a NMR-based protocol designed for Ecometabolomic studies. It provides an unbiased overview of the metabolome of an organism, including polar and nonpolar metabolites, and it facilitates the analysis of many samples, as typically required in ecological studies. In addition to NMR fingerprinting, it provides metabolic profiles, through the identification of primary, secondary and unknown metabolites, applying strategies of elucidation of small molecules typically used in natural-product research.
Metabolomic responses of Quercus ilex seedlings to wounding simulating herbivory
J. Sardans*, A. Gargallo-Garriga, M. Pérez-Trujillo, T. Parella, R. Seco, I. Filella, J. Peñuelas
Plant biology, 2013, 16, 395–403. DOI
Plants defense themselves against herbivory at several levels. One of these levels is the synthesis of inducible chemical defenses. By using NMR metabolomic technique we studied the metabolic changes of plant leaves after a wounding treatment simulating herbivore attack in the Mediterranean sclerophyllous tree Quercus ilex. The study shows the fast metabolic response of Q. ilex to defend its leaves based in a rapid increasing production of quinic acid, quercitol and choline. The results also confirm the suitability of 1H NMR-based metabolomic profiling studies to detect the global metabolome shifts after a biotic stress in tree leaves, and therefore its suitability in ecometabolomic studies.
Strong relationship between elemental stoichiometry and metabolome in plants
A.Rivas-Ubach*, J. Sardans, M. Pérez-Trujillo, M. Estiarte and J. Peñuelas
Proc. Natl. Acad. Sci. USA, 2012, 109, 4181–4186. DOI
Shifts in the elemental stoichiometry of organisms in response to their ontogeny and to changing environmental conditions should be related to metabolomic changes because elements operate mostly as parts of molecular compounds. Here we show this relationship in leaves of Erica multiflora throughout their seasonal development and in response to moderate experimental field conditions of drought and warming. The N/P ratio in leaves decreased in the metabolically active growing seasons, coinciding with an increase in the content of primary metabolites. These results support the growth-rate hypothesis that states that rapidly growing organisms present low N/P ratios because of the increase in allocation of P to RNA. The foliar N/K and P/K ratios were lower in summer and in the drought treatment, in accordance with the role of K in osmotic protection, and coincided with the increase of compounds related to the avoidance of water stress. These results provide strong evidence of the relationship between the changes in foliar C/N/P/K stoichiometry and the changes in the leaf’s metabolome during plant growth and environmental stress. Thus these results represent a step in understanding the relationships between stoichiometry and an organism’s lifestyle.
Chiral Metabonomics: 1H NMR-Based Enantiospecific Differentiation of Metabolites in Human Urine via Direct Cosolvation with β-Cyclodextrin
M. Pérez-Trujillo, J. C. Lindon, T. Parella, H. C. Keun, J. K. Nicholson and T. J. Athersuch*
Analytical Chemistry, 2012, 84, 2868–2874. DOI
Differences in molecular chirality remain an important issue in drug metabolism and pharmacokinetics for the pharmaceutical industry and regulatory authorities and chirality is an important feature of many endogenous metabolites. We present a 1H NMR-based method for the rapid, direct differentiation and identification of chiral drug enantiomers in human urine without pre-treatment of any kind. This approach is simple, rapid, robust, and involves minimal sample manipulation; it avoids labor-intensive steps such as derivatization or purification of the chiral compounds. Moreover, the versatility of NMR spectroscopy allows, after addition of an appropriate CSA, the simultaneous characterization of drug metabolites, both expected and unexpected. From these initial findings we propose that more extensive and detailed enantiospecific metabolic profiling could be possible using CSA-NMR spectroscopy than has been previously reported.
Metabolic Profiling Detects Early Effects of Environmental and Lifestyle Exposure to Cadmium in a Human Population
J. K. Ellis, T. J. Athersuch, L.DK Thomas, F. Teichert, M. Pérez-Trujillo, C. Svendsen, D. J. Spurgeon, R. Singh, L. Järup, J. G. Bundy and H. C. Keun*
BMC Medicine, 2012, 10, 61 . DOI
The ‘exposome’ represents the accumulation of all environmental exposures across a lifetime. Top-down strategies are required to assess something this comprehensive, and could transform our understanding of how environmental factors affect human health. Metabolic profiling (metabonomics / metabolomics) defines an individual’s metabolic phenotype, which is influenced by genotype, diet, lifestyle, health and xenobiotic exposure, and could also reveal intermediate biomarkers for disease risk that reflect adaptive response to exposure. We investigated changes in metabolism in volunteers living near a point source of environmental pollution: a closed zinc smelter with associated elevated levels of environmental cadmium. High-resolution 1H NMR spectroscopy (metabonomics) was used to acquire urinary metabolic profiles from 178 human volunteers.
The study showed evidence that an NMR-based metabolic profiling study in an uncontrolled human population is capable of identifying intermediate biomarkers of response to toxicants at true environmental concentrations, paving the way for exposome research.
