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Gajardo HA, Morales M, Larama G, Luengo-Escobar A, López D, Machado M, Nunes-Nesi A, Reyes-Díaz M, Planchais S, Savouré A, Gago J, Bravo LA. Physiological, transcriptomic and metabolomic insights of three extremophyte woody species living in the multi-stress environment of the Atacama Desert. PLANTA 2024; 260:55. [PMID: 39020000 DOI: 10.1007/s00425-024-04484-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/06/2024] [Indexed: 07/19/2024]
Abstract
MAIN CONCLUSIONS In contrast to Neltuma species, S. tamarugo exhibited higher stress tolerance, maintaining photosynthetic performance through enhanced gene expression and metabolites. Differentially accumulated metabolites include chlorophyll and carotenoids and accumulation of non-nitrogen osmoprotectants. Plant species have developed different adaptive strategies to live under extreme environmental conditions. Hypothetically, extremophyte species present a unique configuration of physiological functions that prioritize stress-tolerance mechanisms while carefully managing resource allocation for photosynthesis. This could be particularly challenging under a multi-stress environment, where the synthesis of multiple and sequential molecular mechanisms is induced. We explored this hypothesis in three phylogenetically related woody species co-occurring in the Atacama Desert, Strombocarpa tamarugo, Neltuma alba, and Neltuma chilensis, by analyzing their leaf dehydration and freezing tolerance and by characterizing their photosynthetic performance under natural growth conditions. Besides, the transcriptomic profiling, biochemical analyses of leaf pigments, and metabolite analysis by untargeted metabolomics were conducted to study gene expression and metabolomic landscape within this challenging multi-stress environment. S. tamarugo showed a higher photosynthetic capacity and leaf stress tolerance than the other species. In this species, a multifactorial response was observed, which involves high photochemical activity associated with a higher content of chlorophylls and β-carotene. The oxidative damage of the photosynthetic apparatus is probably attenuated by the synthesis of complex antioxidant molecules in the three species, but S. tamarugo showed the highest antioxidant capacity. Comparative transcriptomic and metabolomic analyses among the species showed the differential expression of genes involved in the biosynthetic pathways of key stress-related metabolites. Moreover, the synthesis of non-nitrogen osmoprotectant molecules, such as ciceritol and mannitol in S. tamarugo, would allow the nitrogen allocation to support its high photosynthetic capacity without compromising leaf dehydration tolerance and freezing stress avoidance.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Melanie Morales
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Faculty of Biology, University of Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Giovanni Larama
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Ana Luengo-Escobar
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Dariel López
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Mariana Machado
- Departamento de Biología Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biología Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Séverine Planchais
- Institute of Ecology and Environmental Sciences of Paris (iEES), Sorbonne Université, UPEC, CNRS, IRD, INRAE, 75005, Paris, France
| | - Arnould Savouré
- Institute of Ecology and Environmental Sciences of Paris (iEES), Sorbonne Université, UPEC, CNRS, IRD, INRAE, 75005, Paris, France
| | - Jorge Gago
- Research Group On Plant Biology Under Mediterranean Conditions, Departament de Biologia, Universitat de Les Illes Balears/Institute of Agro-Environmental Research and Water Economy-INAGEA, Carretera de Valldemossa, 07122, Palma, Spain
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
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Díaz FP, Dussarrat T, Carrasco-Puga G, Colombié S, Prigent S, Decros G, Bernillon S, Cassan C, Flandin A, Guerrero PC, Gibon Y, Rolin D, Cavieres LA, Pétriacq P, Latorre C, Gutiérrez RA. Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert. THE NEW PHYTOLOGIST 2024; 241:1074-1087. [PMID: 37984856 DOI: 10.1111/nph.19415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.
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Affiliation(s)
- Francisca P Díaz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, 2362807, Valparaíso, Chile
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Thomas Dussarrat
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Gabriela Carrasco-Puga
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Sophie Colombié
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Sylvain Prigent
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Guillaume Decros
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Stéphane Bernillon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Cédric Cassan
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Amélie Flandin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pablo C Guerrero
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos, 8331150, Santiago, Chile
| | - Yves Gibon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Dominique Rolin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Lohengrin A Cavieres
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Claudio Latorre
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
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Boulogne I, Petit P, Desfontaines L, Durambur G, Deborde C, Mirande-Ney C, Arnaudin Q, Plasson C, Grivotte J, Chamot C, Bernard S, Loranger-Merciris G. Biological and Chemical Characterization of Musa paradisiaca Leachate. BIOLOGY 2023; 12:1326. [PMID: 37887036 PMCID: PMC10604775 DOI: 10.3390/biology12101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
There is a growing demand for molecules of natural origin for biocontrol and biostimulation, given the current trend away from synthetic chemical products. Leachates extracted from plantain stems were obtained after biodegradation of the plant material. To characterize the leachate, quantitative determinations of nitrogen, carbon, phosphorus, and cations (K+, Ca2+, Mg2+, Na+), Q2/4, Q2/6, and Q4/6 absorbance ratios, and metabolomic analysis were carried out. The potential role of plantain leachates as fungicide, elicitor of plant defense, and/or plant biostimulant was evaluated by agar well diffusion method, phenotypic, molecular, and imaging approaches. The plant extracts induced a slight inhibition of fungal growth of an aggressive strain of Colletotrichum gloeosporioides, which causes anthracnose. Organic compounds such as cinnamic, ellagic, quinic, and fulvic acids and indole alkaloid such as ellipticine, along with some minerals such as potassium, calcium, and phosphorus, may be responsible for the inhibition of fungal growth. In addition, jasmonic, benzoic, and salicylic acids, which are known to play a role in plant defense and as biostimulants in tomato, were detected in leachate extract. Indeed, foliar application of banana leachate induced overexpression of LOXD, PPOD, and Worky70-80 genes, which are involved in phenylpropanoid metabolism, jasmonic acid biosynthesis, and salicylic acid metabolism, respectively. Leachate also activated root growth in tomato seedlings. However, the main impact of the leachate was observed on mature plants, where it caused a reduction in leaf area and fresh weight, the remodeling of stem cell wall glycopolymers, and an increase in the expression of proline dehydrogenase.
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Affiliation(s)
- Isabelle Boulogne
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Philippe Petit
- Université des Antilles, UMR ISYEB-MNHN-CNRS-Sorbonne Université-EPHE, UFR Sciences Exactes et Naturelles, Campus de Fouillole, F-97157 Pointe-à-Pitre, Guadeloupe, France;
| | | | - Gaëlle Durambur
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Catherine Deborde
- INRAE, PROBE Research Infrastructure, BIBS Facility, F-44300 Nantes, France;
- INRAE, UR1268 BIA Biopolymères Interactions Assemblages F-44300 Nantes, France
| | - Cathleen Mirande-Ney
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Quentin Arnaudin
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Carole Plasson
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Julie Grivotte
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Christophe Chamot
- Université de Rouen Normandie, Normandie Univ, INSERM, CNRS, HeRacLeS US 51 UAR 2026, PRIMACEN, F-76000 Rouen, France;
| | - Sophie Bernard
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
- Université de Rouen Normandie, Normandie Univ, INSERM, CNRS, HeRacLeS US 51 UAR 2026, PRIMACEN, F-76000 Rouen, France;
| | - Gladys Loranger-Merciris
- Université des Antilles, UMR ISYEB-MNHN-CNRS-Sorbonne Université-EPHE, UFR Sciences Exactes et Naturelles, Campus de Fouillole, F-97157 Pointe-à-Pitre, Guadeloupe, France;
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Dussarrat T, Schweiger R, Ziaja D, Nguyen TTN, Krause L, Jakobs R, Eilers EJ, Müller C. Influences of chemotype and parental genotype on metabolic fingerprints of tansy plants uncovered by predictive metabolomics. Sci Rep 2023; 13:11645. [PMID: 37468576 DOI: 10.1038/s41598-023-38790-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Intraspecific plant chemodiversity shapes plant-environment interactions. Within species, chemotypes can be defined according to variation in dominant specialised metabolites belonging to certain classes. Different ecological functions could be assigned to these distinct chemotypes. However, the roles of other metabolic variation and the parental origin (or genotype) of the chemotypes remain poorly explored. Here, we first compared the capacity of terpenoid profiles and metabolic fingerprints to distinguish five chemotypes of common tansy (Tanacetum vulgare) and depict metabolic differences. Metabolic fingerprints captured higher variation in metabolites while preserving the ability to define chemotypes. These differences might influence plant performance and interactions with the environment. Next, to characterise the influence of the maternal origin on chemodiversity, we performed variation partitioning and generalised linear modelling. Our findings revealed that maternal origin was a higher source of chemical variation than chemotype. Predictive metabolomics unveiled 184 markers predicting maternal origin with 89% accuracy. These markers included, among others, phenolics, whose functions in plant-environment interactions are well established. Hence, these findings place parental genotype at the forefront of intraspecific chemodiversity. We recommend considering this factor when comparing the ecology of various chemotypes. Additionally, the combined inclusion of inherited variation in main terpenoids and other metabolites in computational models may help connect chemodiversity and evolutionary principles.
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Affiliation(s)
- Thomas Dussarrat
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
| | - Rabea Schweiger
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Dominik Ziaja
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Thuan T N Nguyen
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Liv Krause
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Ruth Jakobs
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Elisabeth J Eilers
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- CTL GmbH Bielefeld, Krackser Straße 12, 33659, Bielefeld, Germany
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Dollinger J, Pétriacq P, Flandin A, Samouelian A. Soil metabolomics: A powerful tool for predicting and specifying pesticide sorption. CHEMOSPHERE 2023:139302. [PMID: 37385484 DOI: 10.1016/j.chemosphere.2023.139302] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
Sorption regulates the dispersion of pesticides from cropped areas to surrounding water bodies as well as their persistence. Assessing the risk of water contamination and evaluating the efficiency of mitigation measures, requires fine-resolution sorption data and a good knowledge of its drivers. This study aimed to assess the potential of a new approach combining chemometric and soil metabolomics to estimate the adsorption and desorption coefficients of a range of pesticides. It also aims to identify and characterise key components of soil organic matter (SOM) driving the sorption of these pesticides. We constituted a dataset of 43 soils from Tunisia, France and Guadeloupe (West Indies), covering extensive ranges of texture, organic carbon and pH. We performed untargeted soil metabolomics by liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS). We measured the adsorption and desorption coefficients of three pesticides namely glyphosate, 2,4-D and difenoconazole for these soils. We developed Partial Least Square Regression (PLSR) models for the prediction of the sorption coefficients from the RT-m/z matrix and conducted further ANOVA analyses to identify, annotate and characterise the most significant constituents of SOM in the PLSR models. The curated metabolomics matrix yielded 1213 metabolic markers. The prediction performance of the PLSR models was generally high for the adsorption coefficients Kdads (0.3 < R2 < 0.8) and for the desorption coefficients Kfdes (0.6 < R2 < 0.8) but low for ndes (0.03 < R2 < 0.3). The most significant features in the predictive models were annotated with a confidence level of 2 or 3. The molecular descriptors of these putative compounds suggest that the pool of SOM compounds driving glyphosate sorption is reduced compared to 2,4-D and difenoconazole, and these compounds are generally more polar. This approach can provide estimates of the adsorption and desorption coefficients of pesticides, including polar pesticide, for contrasted pedoclimates.
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Affiliation(s)
- Jeanne Dollinger
- UMR LISAH, Université Montpellier, INRAE, IRD, Institut Agro, 34060, Montpellier, France.
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR1332, BFP, 33882, Villenave d'Ornon, France; Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Amélie Flandin
- Univ. Bordeaux, INRAE, UMR1332, BFP, 33882, Villenave d'Ornon, France; Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Anatja Samouelian
- UMR LISAH, Université Montpellier, INRAE, IRD, Institut Agro, 34060, Montpellier, France
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De León LF, Silva B, Avilés-Rodríguez KJ, Buitrago-Rosas D. Harnessing the omics revolution to address the global biodiversity crisis. Curr Opin Biotechnol 2023; 80:102901. [PMID: 36773576 DOI: 10.1016/j.copbio.2023.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/12/2023]
Abstract
Human disturbances are altering global biodiversity in unprecedented ways. We identify three fundamental challenges underpinning our understanding of global biodiversity (namely discovery, loss, and preservation), and discuss how the omics revolution (e.g. genomics, transcriptomics, proteomics, metabolomics, and meta-omics) can help address these challenges. We also discuss how omics tools can illuminate the major drivers of biodiversity loss, including invasive species, pollution, urbanization, overexploitation, and climate change, with a special focus on highly diverse tropical environments. Although omics tools are transforming the traditional toolkit of biodiversity research, their application to addressing the current biodiversity crisis remains limited and may not suffice to offset current rates of biodiversity loss. Despite technical and logistical challenges, omics tools need to be fully integrated into global biodiversity research, and better strategies are needed to improve their translation into biodiversity policy and practice. It is also important to recognize that although the omics revolution can be considered the biologist's dream, socioeconomic disparity limits their application in biodiversity research.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
| | - Bruna Silva
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kevin J Avilés-Rodríguez
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA; Department of Biology, Fordham University, Bronx, NY, USA
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Shen S, Zhan C, Yang C, Fernie AR, Luo J. Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives. MOLECULAR PLANT 2023; 16:43-63. [PMID: 36114669 DOI: 10.1016/j.molp.2022.09.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.
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Affiliation(s)
- Shuangqian Shen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chenkun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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Couée I. Interplay of Methodology and Conceptualization in Plant Abiotic Stress Signaling. Methods Mol Biol 2023; 2642:3-22. [PMID: 36944870 DOI: 10.1007/978-1-0716-3044-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Characterizing the mechanisms of plant sensitivity and reactivity to physicochemical cues related to abiotic stresses is of utmost importance for understanding plant-environment interactions, adaptations of the sessile lifestyle, and the evolutionary dynamics of plant species and populations. Moreover, plant communities are confronted with an environmental context of global change, involving climate changes, planetary pollutions of soils, waters and atmosphere, and additional anthropogenic changes. The mechanisms through which plants perceive abiotic stress stimuli and transduce stress perception into physiological responses constitute the primary line of interaction between the plant and the environment, and therefore between the plant and global changes. Understanding how plants perceive complex combinations of abiotic stress signals and transduce the resulting information into coordinated responses of abiotic stress tolerance is therefore essential for devising genetic, agricultural, and agroecological strategies that can ensure climate change resilience, global food security, and environmental protection. Discovery and characterization of sensing and signaling mechanisms of plant cells are usually carried out within the general framework of eukaryotic sensing and signal transduction. However, further progress depends on a close relationship between the conceptualization of sensing and signaling processes with adequate methodologies and techniques that encompass biochemical and biophysical approaches, cell biology, molecular biology, and genetics. The integration of subcellular and cellular analyses as well as the integration of in vitro and in vivo analyses are particularly important to evaluate the efficiency of sensing and signaling mechanisms in planta. Major progress has been made in the last 10-20 years with the caveat that cell-specific processes and in vivo processes still remain difficult to analyze and with the additional caveat that the range of plant models under study remains rather limited relatively to plant biodiversity and to the diversity of stress situations.
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Affiliation(s)
- Ivan Couée
- UMR 6553 ECOBIO (Ecosystems-Biodiversity-Evolution), Centre National de la Recherche Scientifique (CNRS), University of Rennes, Rennes, France.
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Bruňáková K, Bálintová M, Petijová L, Čellárová E. Does phenotyping of Hypericum secondary metabolism reveal a tolerance to biotic/abiotic stressors? FRONTIERS IN PLANT SCIENCE 2022; 13:1042375. [PMID: 36531362 PMCID: PMC9748567 DOI: 10.3389/fpls.2022.1042375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
In this review we summarize the current knowledge about the changes in Hypericum secondary metabolism induced by biotic/abiotic stressors. It is known that the extreme environmental conditions activate signaling pathways leading to triggering of enzymatic and non-enzymatic defense systems, which stimulate production of secondary metabolites with antioxidant and protective effects. Due to several groups of bioactive compounds including naphthodianthrones, acylphloroglucinols, flavonoids, and phenylpropanes, the world-wide Hypericum perforatum represents a high-value medicinal crop of Hypericum genus, which belongs to the most diverse genera within flowering plants. The summary of the up-to-date knowledge reveals a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance. The chlorogenic acid, and flavonoids, namely the amentoflavone, quercetin or kaempferol glycosides have been reported as the most defense-related metabolites associated with plant tolerance against stressful environment including temperature, light, and drought, in association with the biotic stimuli resulting from plant-microbe interactions. As an example, the species-specific cold-induced phenolics profiles of 10 Hypericum representatives of different provenances cultured in vitro are illustrated in the case-study. Principal component analysis revealed a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance indicating a link between the provenance of Hypericum species and inherent mechanisms of cold tolerance. The underlying metabolome alterations along with the changes in the activities of ROS-scavenging enzymes, and non-enzymatic physiological markers are discussed. Given these data it can be anticipated that some Hypericum species native to divergent habitats, with interesting high-value secondary metabolite composition and predicted high tolerance to biotic/abiotic stresses would attract the attention as valuable sources of bioactive compounds for many medicinal purposes.
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