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Jardinaud MF, Carrere S, Gourion B, Gamas P. Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant Is Highly Dependent on Sinorhizobium Strains. PLANT & CELL PHYSIOLOGY 2023; 64:27-42. [PMID: 36151948 DOI: 10.1093/pcp/pcac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula, SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1, although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene.
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Affiliation(s)
- Marie-Françoise Jardinaud
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Sebastien Carrere
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Benjamin Gourion
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Pascal Gamas
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
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Yang M, Luo F, Song Y, Ma S, Ma Y, Fazal A, Yin T, Lu G, Sun S, Qi J, Wen Z, Li Y, Yang Y. The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities. Microb Biotechnol 2022; 15:2942-2957. [PMID: 36336802 PMCID: PMC9733649 DOI: 10.1111/1751-7915.14164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate-treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil-plant continuum largely control the composition and function of the root-associated microbiome of triple transgenic soybean.
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Affiliation(s)
- Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Fuhe Luo
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Yuchen Song
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Shenglin Ma
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Yudi Ma
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Tongming Yin
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- School of Life SciencesHuaiyin Normal UniversityHuaianChina
| | - Shucun Sun
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, College of Environmental and Resource SciencesZhejiang A&F UniversityHangzhouChina
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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Medicago-Sinorhizobium-Ralstonia Co-infection Reveals Legume Nodules as Pathogen Confined Infection Sites Developing Weak Defenses. Curr Biol 2020; 30:351-358.e4. [DOI: 10.1016/j.cub.2019.11.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/02/2019] [Accepted: 11/21/2019] [Indexed: 11/20/2022]
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Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A. Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome. PLoS Comput Biol 2015; 11:e1004478. [PMID: 26340565 PMCID: PMC4560400 DOI: 10.1371/journal.pcbi.1004478] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 07/24/2015] [Indexed: 11/21/2022] Open
Abstract
Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial pangenomes. The influence of transcriptional regulatory networks on the evolution of bacterial pangenomes has not yet been elucidated, even though the role of transcriptional regulation is widely recognized. Using the model symbiont Sinorhizobium meliloti we have predicted the regulatory targets of 41 transcription factors in 51 strains and 5 other rhizobial species, showing a correlation between regulon diversity and pangenome evolution, through upstream sequence diversity and accessory genome composition. We have also shown that genes not wired to the regulatory network are more likely to belong to the accessory genome, thus suggesting that inclusion in the regulatory circuits may be an indicator of gene conservation. We have also highlighted a series of transcription factors that preferentially regulate genes belonging to one of the three replicons of this species, indicating the presence of replicon-specific regulatory modules, with peculiar functional signatures. At the same time the chromid shares a significant part of the regulatory network with the chromosome, indicating an additional way by which this replicon integrates itself in the pangenome.
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Affiliation(s)
- Marco Galardini
- Department of Biology, University of Florence, Florence, Italy
| | - Matteo Brilli
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
| | - Giulia Spini
- Dipartimento di Biotecnologie Agrarie, Sezione di Microbiologia, University of Florence, Florence, Italy
| | - Matteo Rossi
- Department of Biology, University of Florence, Florence, Italy
| | | | - Alessia Bani
- Department of Biology, University of Florence, Florence, Italy
| | | | - Marco Moretto
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
| | - Kristof Engelen
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Rome, Italy
| | - Francesco Pini
- Interdisciplinary Research Institute USR3078, CNRS-Universit Lille Nord de France, Villeneuve d’Ascq, France
| | - Emanuele G. Biondi
- Interdisciplinary Research Institute USR3078, CNRS-Universit Lille Nord de France, Villeneuve d’Ascq, France
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
- * E-mail:
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Molina-Sánchez MD, López-Contreras JA, Toro N, Fernández-López M. Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region. SPRINGERPLUS 2015; 4:259. [PMID: 26090306 PMCID: PMC4468178 DOI: 10.1186/s40064-015-1062-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/26/2015] [Indexed: 11/10/2022]
Abstract
The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti has been widely studied due to its ability to improve crop yields through direct interactions with leguminous plants. S. meliloti AK21 is a wild type strain that forms nodules on Medicago plants in saline and drought conditions in the Aral Sea Region. The aim of this work was to establish the genetic similarities and differences between S. meliloti AK21 and the reference strain S. meliloti 1021. Comparative genome hybridization with the model reference strain S. meliloti 1021 yielded 365 variable genes, grouped into 11 regions in the three main replicons in S. meliloti AK21. The most extensive regions of variability were found in the symbiotic plasmid pSymA, which also contained the largest number of orthologous and polymorphic sequences identified by suppression subtractive hybridization. This procedure identified a large number of divergent sequences and others without homology in the databases, the further investigation of which could provide new insight into the alternative metabolic pathways present in S. meliloti AK21. We identified a plasmid replication module from the repABC replicon family, together with plasmid mobilization-related genes (traG and a VirB9-like protein), which suggest that this indigenous isolate harbors an accessory plasmid. Furthermore, the transcriptomic profiles reflected differences in gene content and regulation between S. meliloti AK21 and S. meliloti 1021 (ExpR and PhoB regulons), but provided evidence for an as yet unknown, alternative mechanism involving activation of the cbb3 terminal oxidase. Finally, phenotypic microarrays characterization revealed a greater versatility of substrate use and chemical degradation than for S. meliloti 1021.
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Affiliation(s)
- María Dolores Molina-Sánchez
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
| | - José Antonio López-Contreras
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Manuel Fernández-López
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
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