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Fu Y, Mason AS, Song M, Ni X, Liu L, Shi J, Wang T, Xiao M, Zhang Y, Fu D, Yu H. Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus. Cell Mol Biol Lett 2023; 28:63. [PMID: 37543634 PMCID: PMC10404376 DOI: 10.1186/s11658-023-00479-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/20/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown. METHODS Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses. RESULTS Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency. CONCLUSIONS Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Maolin Song
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Xiyuan Ni
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lei Liu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianghua Shi
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tanliu Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yaofeng Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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Cera A, Montserrat‐Martí G, Drenovsky RE, Ourry A, Brunel‐Muguet S, Palacio S. Gypsum endemics accumulate excess nutrients in leaves as a potential constitutive strategy to grow in grazed extreme soils. PHYSIOLOGIA PLANTARUM 2022; 174:e13738. [PMID: 35765177 PMCID: PMC9546198 DOI: 10.1111/ppl.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Extreme soils often have mineral nutrient imbalances compared to plant nutritional requirements and co-occur in open areas where grazers thrive. Thus, plants must respond to both constraints, which can affect nutrient concentrations in all plant organs. Gypsum soil provides an excellent model system to study adaptations to extreme soils under current grazing practices as it harbours two groups of plant species that differ in their tolerance to gypsum soils and foliar composition. However, nutrient concentrations in organs other than leaves, and their individual responses to simulated herbivory, are still unknown in gypsum plants. We studied plant biomass, root mass ratio and nutrient partitioning among different organs (leaves, stems, coarse roots, fine roots) in five gypsum endemics and five generalists cultivated in gypsum and calcareous soils and subjected to different levels of simulated browsing. Gypsum endemics tended to have higher elemental concentration in leaves, stems and coarse roots than generalist species in both soil types, whereas both groups tended to show similar high concentrations in fine roots. This behaviour was especially clear with sulphur (S), which is found in excess in gypsum soils, and which endemics accumulated in leaves as sulphate (>50% of S). Moreover, plants subjected to clipping, regardless of their affinity to gypsum, were unable to compensate for biomass losses and showed similar elemental composition to unclipped plants. The accumulation of excess mineral nutrients by endemic species in aboveground organs may be a constitutive nutritional strategy in extreme soils and is potentially playing an anti-herbivore role in grazed gypsum outcrops.
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Affiliation(s)
- Andreu Cera
- Departamento Biodiversidad y Restauración, Instituto Pirenaico de EcologíaConsejo Superior de Investigaciones CientíficasJacaSpain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Secció de Botànica i Micologia, Facultat de BiologiaUniversitat de BarcelonaBarcelonaSpain
| | - Gabriel Montserrat‐Martí
- Departamento Biodiversidad y Restauración, Instituto Pirenaico de EcologíaConsejo Superior de Investigaciones CientíficasZaragozaSpain
| | | | - Alain Ourry
- Agronomie et Nutritions N, C, S, SFR Normandie Végétal (FED 4277), UNICAEN, INRAE, UMR 950 Ecophysiologie VégétaleNormandie UniversitéCaenFrance
| | - Sophie Brunel‐Muguet
- Agronomie et Nutritions N, C, S, SFR Normandie Végétal (FED 4277), UNICAEN, INRAE, UMR 950 Ecophysiologie VégétaleNormandie UniversitéCaenFrance
| | - Sara Palacio
- Departamento Biodiversidad y Restauración, Instituto Pirenaico de EcologíaConsejo Superior de Investigaciones CientíficasJacaSpain
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D’Oria A, Jing L, Arkoun M, Pluchon S, Pateyron S, Trouverie J, Etienne P, Diquélou S, Ourry A. Transcriptomic, Metabolomic and Ionomic Analyses Reveal Early Modulation of Leaf Mineral Content in Brassica napus under Mild or Severe Drought. Int J Mol Sci 2022; 23:781. [PMID: 35054964 PMCID: PMC8776245 DOI: 10.3390/ijms23020781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
While it is generally acknowledged that drought is one of the main abiotic factors affecting plant growth, how mineral nutrition is specifically and negatively affected by water deficit has received very little attention, other than being analyzed as a consequence of reduced growth. Therefore, Brassica napus plants were subjected to a gradual onset of water deficits (mild, severe, or severe extended), and leaves were analyzed at the ionomic, transcriptomic and metabolic levels. The number of Differentially Expressed Genes (DEGs) and of the most differentially accumulated metabolites increased from mild (525 DEGs, 57 metabolites) to severe (5454 DEGs, 78 metabolites) and severe extended (9346 DEGs, 95 metabolites) water deficit. Gene ontology enrichment analysis of the 11,747 DEGs identified revealed that ion transport was one of the most significant processes affected, even under mild water deficit, and this was also confirmed by the shift in ionomic composition (mostly micronutrients with a strong decrease in Mo, Fe, Zn, and Mn in leaves) that occurred well before growth reduction. The metabolomic data and most of the transcriptomic data suggested that well-known early leaf responses to drought such as phytohormone metabolism (ABA and JA), proline accumulation, and oxidative stress defense were induced later than repression of genes related to nutrient transport.
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Affiliation(s)
- Aurélien D’Oria
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France; (M.A.); (S.P.)
| | - Lun Jing
- Plateformes Analytiques de Recherche, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France;
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France; (M.A.); (S.P.)
| | - Sylvain Pluchon
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France; (M.A.); (S.P.)
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Jacques Trouverie
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
| | - Philippe Etienne
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
| | - Sylvain Diquélou
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
| | - Alain Ourry
- Unicaen, INRAE, UMR 950 Eva, SFR Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (A.D.); (J.T.); (P.E.); (S.D.)
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Jacquiod S, Spor A, Wei S, Munkager V, Bru D, Sørensen SJ, Salon C, Philippot L, Blouin M. Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes. Ecol Lett 2021; 25:189-201. [PMID: 34749426 DOI: 10.1111/ele.13916] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Artificial selection of microbiota opens new avenues for improving plants. However, reported results lack consistency. We hypothesised that the success in artificial selection of microbiota depends on the stabilisation of community structure. In a ten-generation experiment involving 1,800 plants, we selected rhizosphere microbiota of Brachypodium distachyon associated with high or low leaf greenness, a proxy of plant performance. The microbiota structure showed strong fluctuations during an initial transitory phase, with no detectable leaf greenness heritability. After five generations, the microbiota structure stabilised, concomitantly with heritability in leaf greenness. Selection, initially ineffective, did successfully alter the selected property as intended, especially for high selection. We show a remarkable correlation between the variability in plant traits and selected microbiota structures, revealing two distinct sub-communities associated with high or low leaf greenness, whose abundance was significantly steered by directional selection. Understanding microbiota structure stabilisation will improve the reliability of artificial microbiota selection.
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Affiliation(s)
- Samuel Jacquiod
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Aymé Spor
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Shaodong Wei
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Victoria Munkager
- Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - David Bru
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Salon
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Laurent Philippot
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Manuel Blouin
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
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Comparative Omics Analysis of Brassica napus Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles. Int J Mol Sci 2021; 22:ijms222111679. [PMID: 34769110 PMCID: PMC8584284 DOI: 10.3390/ijms222111679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of Brassica napus roots to characterize the effects of six individual macronutrient deprivations (N, Mg, P, S, K, and Ca). Our results showed that before any visual phenotypic response, all macronutrient deprivations led to a large modulation of the transcriptome and metabolome involved in various metabolic pathways, and some were common to all macronutrient deprivations. Significantly, comparative transcriptomic analysis allowed the definition of a subset of 3282, 2011, 6325, 1384, 439, and 5157 differentially expressed genes (DEGs) specific to N, Mg, P, S, K, and Ca deprivations, respectively. Surprisingly, gene ontology term enrichment analysis performed on this subset of specific DEGs highlighted biological processes that are common to a number of these macronutrient deprivations, illustrating the complexity of nutrient interactions. In addition, a set of 38 biochemical compounds that discriminated the macronutrient deprivations was identified using a metabolic approach. The opportunity to use these specific DEGs and/or biochemical compounds as potential molecular indicators to diagnose macronutrient deficiency is discussed.
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Lornac A, Havé M, Chardon F, Soulay F, Clément G, Avice JC, Masclaux-Daubresse C. Autophagy Controls Sulphur Metabolism in the Rosette Leaves of Arabidopsis and Facilitates S Remobilization to the Seeds. Cells 2020; 9:E332. [PMID: 32023971 PMCID: PMC7073174 DOI: 10.3390/cells9020332] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/15/2023] Open
Abstract
Sulphur deficiency in crops became an agricultural concern several decades ago, due to the decrease of S deposition and the atmospheric sulphur dioxide emissions released by industrial plants. Autophagy, which is a conserved mechanism for nutrient recycling in eukaryotes, is involved in nitrogen, iron, zinc and manganese remobilizations from the rosette to the seeds in Arabidopsis thaliana. Here, we have compared the role of autophagy in sulphur and nitrogen management at the whole plant level, performing concurrent labelling with 34S and 15N isotopes on atg5 mutants and control lines. We show that both 34S and 15N remobilizations from the rosette to the seeds are impaired in the atg5 mutants irrespective of salicylic acid accumulation and of sulphur nutrition. The comparison in each genotype of the partitions of 15N and 34S in the seeds (as % of the whole plant) indicates that the remobilization of 34S to the seeds was twice more efficient than that of 15N in both autophagy mutants and control lines under high S conditions, and also in control lines under low S conditions. This was different in the autophagy mutants grown under low S conditions. Under low S, the partition of 34S to their seeds was indeed not twice as high but similar to that of 15N. Such discrepancy shows that when sulphate availability is scarce, autophagy mutants display stronger defects for 34S remobilization relative to 15N remobilization than under high S conditions. It suggests, moreover, that autophagy mainly affects the transport of N-poor S-containing molecules and possibly sulphate.
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Affiliation(s)
- Aurélia Lornac
- UCBN, UMR INRA–UCBN 950 Ecophysiologie Végétale &, Agronomie & Nutritions N.C.S., SFR Normandie Végétal (FED 4277), Normandie Université, F-14032 Caen, France
| | - Marien Havé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Fabien Chardon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Fabienne Soulay
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Jean-Christophe Avice
- UCBN, UMR INRA–UCBN 950 Ecophysiologie Végétale &, Agronomie & Nutritions N.C.S., SFR Normandie Végétal (FED 4277), Normandie Université, F-14032 Caen, France
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
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